# Siftome Ranked Dataset Export

Active GEO index contains 47389 ranked datasets; organism mixed: Homo sapiens (35667), Mus musculus (11722); assay type mixed: microarray (24601), bulk RNA-seq (22787), other assay type (1). Rankings use the Tumor vs normal comparison with transparent suitability, metadata quality, and warning rules.

Exploratory machine assessment; not a reviewed, frozen cohort or analysis approval. Study totals and cohort membership counts are not query-eligible sample counts. Unavailable eligibility evidence is unknown.

Results are a starting point for review. Missing evidence leaves suitability unknown.

## Citation and Provenance

- **Product:** Siftome
- **Generated date:** 2026-10-27T11:44:13.967849853Z
- **Citation text:** Generated with Siftome, a public omics dataset triage and metadata quality workflow tool.
- **Original source citation reminder:** Cite original dataset sources when exported results are used in publications.
- **Search criteria summary:** Patient tissue tumor-vs-normal; active defaults: none; user modifications: relaxed defaults: Human only; Bulk RNA-seq only; Tumor-normal only; Tissue or biopsy only; Hide biofluid/model systems; additional filters: Disease: Sepsis
- **Structured search criteria:** searchIntent=patient-tissue-tumor-normal; recommendedOnly=false; excludeLowMetadataQuality=false; minimumSampleCount=none; processedDataAvailableOnly=false; hideCellLineDatasets=false; hideAmbiguousGroupings=false; matchedNormalOnly=false; geoOnly=false; recount3AvailableOnly=false; expressionAtlasAvailableOnly=false; trustedProcessedCountsAvailableOnly=false; tumorNormalOnly=false; tissueOrBiopsyOnly=false; hideBiofluidAndModelSystems=false; biofluidOnly=false; treatmentControlOnly=false; humanOnly=false; mouseOnly=false; bulkRnaSeqOnly=false; microarrayOnly=false; targetDiseaseContextOnly=false; includeBroaderGiAndMultiCancer=false; query=none; diseaseCondition=Sepsis; tissue=none; organism=none; assayType=none; modelType=none; anatomicalSource=none; specimenMaterial=none; cellPopulation=none
- **Intent-specific ranking notice:** Recommendations are specific to the Patient tissue tumor-vs-normal intent and are not globally valid across all biological questions.
- **Active organism expectation:** Homo sapiens
- **Active assay expectation:** bulk RNA-seq
- **Active default filters:** none
- **User-modified filters:** relaxed defaults: Human only; Bulk RNA-seq only; Tumor-normal only; Tissue or biopsy only; Hide biofluid/model systems; additional filters: Disease: Sepsis
- **Ranking batch:** 806958966744631c40063f0fc890965facdd40c0daba51edc35cd7d4956e097f
- **Ranking batch ID:** d20028fc-f826-48f6-9cf2-e0eef07b824f
- **Candidate generation version:** parent-series-search-candidates-v1
- **Candidate counts:** total=49115, parent=49115, secondary=0
- **Candidate set fingerprint:** d89295ea9fc12132672e2de3bcfe4afb86efc004cd3ab3c563538908e637a647
- **Search intent:** patient-tissue-tumor-normal
- **Intent behavior version:** search-intent-behavior-v5
- **Scoring version:** intent-aware-scoring-v46
- **Normalization version:** sample-biological-dimensions-v26
- **Warning version:** intent-aware-warnings-v13
- **Ranking created at:** 2026-10-27T02:51:59.521293Z
- **Source import or snapshot date:** Active GEO index snapshot for ranking batch 806958966744631c40063f0fc890965facdd40c0daba51edc35cd7d4956e097f
- **Recommendation label definitions:** Recommended: strong first-pass triage candidate for the active criteria.; Useful with caution: potentially relevant but requires manual review of warnings and context.; Not suitable: not recommended for the active criteria without substantial manual justification.; Exploratory only: useful for discovery or review, not a direct recommendation.
- **Recommendation-label meanings:** Recommended: strong first-pass triage candidate for the active criteria.; Useful with caution: potentially relevant but requires manual review of warnings and context.; Not suitable: not recommended for the active criteria without substantial manual justification.; Exploratory only: useful for discovery or review, not a direct recommendation.
- **Known warning limitations:** Warnings are rule-based metadata signals, not a replacement for manual sample review before analysis.

## Search Criteria

- **Search version:** tiered-discovery-search-v12
- **Scoring version:** intent-aware-scoring-v46
- **Intent behavior version:** search-intent-behavior-v5
- **Search intent:** Patient tissue tumor-vs-normal
- **Intent-specific ranking notice:** Recommendations are specific to the Patient tissue tumor-vs-normal intent and are not globally valid across all biological questions.
- **Intent wording:** Ranks human tissue tumor-vs-normal GEO datasets for suitability triage.
- **Active organism expectation:** Homo sapiens
- **Active assay expectation:** bulk RNA-seq
- **Active default filters:** none
- **User-modified filters:** relaxed defaults: Human only; Bulk RNA-seq only; Tumor-normal only; Tissue or biopsy only; Hide biofluid/model systems; additional filters: Disease: Sepsis
- **Active assay mix:** bulk RNA-seq
- **Active default filter state:** {"labels": ["Human only", "Bulk RNA-seq only", "Tumor-normal only", "Tissue or biopsy only", "Hide biofluid/model systems"], "summary": "Human only; Bulk RNA-seq only; Tumor-normal only; Tissue or biopsy only; Hide biofluid/model systems", "humanOnly": true, "mouseOnly": false, "biofluidOnly": false, "bulkRnaSeqOnly": true, "microarrayOnly": false, "recommendedOnly": false, "tumorNormalOnly": true, "matchedNormalOnly": false, "tissueOrBiopsyOnly": true, "treatmentControlOnly": false, "targetDiseaseContextOnly": false, "hideBiofluidAndModelSystems": true}
- **Allowed study designs:** tumor vs matched normal or tumor vs unmatched normal
- **Recommendation meaning:** Recommended means a human bulk RNA-seq tissue or biopsy cohort with clear tumor-normal grouping and sufficient metadata for first-pass triage.
- **Recommendation-label meanings:** Recommended: strong first-pass triage candidate for the active criteria.; Useful with caution: potentially relevant but requires manual review of warnings and context.; Not suitable: not recommended for the active criteria without substantial manual justification.; Exploratory only: useful for discovery or review, not a direct recommendation.
- **Known warning limitations:** Warnings are rule-based metadata signals, not a replacement for manual sample review before analysis.
- **Source:** GEO
- **Active index organism:** mixed: Homo sapiens (35667), Mus musculus (11722)
- **Active index assay type:** mixed: microarray (24601), bulk RNA-seq (22787), other assay type (1)
- **Search use case:** Ranks human tissue tumor-vs-normal GEO datasets for suitability triage.
- **Minimum sample count:** none
- **Processed data available only:** false
- **Required metadata:** usable sample-level metadata
- **Disallowed contexts:** microarray unless explicitly enabled, biofluid-only datasets, cell-line datasets, organoid datasets, xenograft or PDX datasets, or treatment-only experiments

## Ranked Datasets

| Rank | Dataset | Title | Unmet criteria | Design | Specimen | Scores | Warnings | Source | Recommendation |
| ---: | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| 1 | [GSE142255](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142255) | Gene expression profiling of immune cells from patients with acute on chronic liver failure (ACLF) | none | Patient biofluid vs healthy control | Biofluid | suitability 20; metadata 100; overall 45 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142255) | Exploratory only |
| 2 | [GSE205672](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE205672) | Transcriptomes of human PBMCs and monocytes in sepsis patients | none | Patient biofluid vs healthy control | Biofluid | suitability 20; metadata 100; overall 45 | none | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE205672) | Exploratory only |
| 3 | [GSE208092](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208092) | Transcriptome analysis to explore the shared and distinct immune signature between severe COVID-19 and bacterial sepsis | none | Patient biofluid vs healthy control | Biofluid | suitability 20; metadata 100; overall 45 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208092) | Exploratory only |
| 4 | [GSE217700](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE217700) | Analysis of Immune and Prognostic-Related lncRNA PRKCQ-AS1 for Predicting Prognosis and Regulating Effect in Sepsis | none | Patient biofluid vs healthy control | Biofluid | suitability 20; metadata 100; overall 45 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE217700) | Exploratory only |
| 5 | [GSE26378](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26378) | Expression data from validation cohort of children with septic shock | none | Patient biofluid vs healthy control | Biofluid | suitability 20; metadata 100; overall 45 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26378) | Exploratory only |
| 6 | [GSE26440](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26440) | Expression data for derivation of septic shock subgroups | none | Patient biofluid vs healthy control | Biofluid | suitability 20; metadata 100; overall 45 | AMBIGUOUS_SAMPLES_DETECTED [info]: Ambiguous sample metadata was detected in 32 sample(s): GSM648630 matched "group: n/a"; GSM648631 matched "group: n/a"; GSM648632 matched "group: n/a"; additional ambiguous samples omitted. Review these samples before inclusion or manual group assignment.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26440) | Exploratory only |
| 7 | [GSE294985](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294985) | Transcriptomes of human whole blood cells in sepsis patients | none | Patient biofluid vs healthy control | Biofluid | suitability 20; metadata 100; overall 45 | none | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294985) | Exploratory only |
| 8 | [GSE60424](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60424) | Next generation sequencing of human immune cell subsets across diseases | none | Patient biofluid vs healthy control | Biofluid | suitability 20; metadata 100; overall 45 | none | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60424) | Exploratory only |
| 9 | [GSE69063](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE69063) | Gene expression patterns in blood during human anaphylaxis, trauma, and sepsis | none | Patient biofluid vs healthy control | Biofluid | suitability 20; metadata 100; overall 45 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE69063) | Exploratory only |
| 10 | [GSE80496](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE80496) | Diagnosis of childhood bacterial and viral infection using host RNA expression - Meningococcal validation cohort | none | Patient biofluid vs healthy control | Biofluid | suitability 20; metadata 100; overall 45 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE80496) | Exploratory only |
| 11 | [GSE134347](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134347) | Protein-coding and non-coding RNA expression in whole blood leukocytes of healthy subjects and critically-ill patients with sepsis or non-infectious etiology. | none | Patient biofluid vs healthy control | Biofluid | suitability 10; metadata 100; overall 45 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134347) | Exploratory only |
| 12 | [GSE137340](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137340) | Blood transcriptome of human sepsis in an Indian cohort [Illumina array] | none | Patient biofluid vs healthy control | Biofluid | suitability 10; metadata 100; overall 45 | AMBIGUOUS_SAMPLES_DETECTED [info]: Ambiguous sample metadata was detected in 2 sample(s): GSM4075803 matched "diagnosis: NA"; GSM4075804 matched "diagnosis: NA". Review these samples before inclusion or manual group assignment.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137340) | Exploratory only |
| 13 | [GSE185263](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE185263) | Predicting sepsis severity at first clinical presentation: the role of endotypes and mechanistic signatures | none | Patient biofluid vs healthy control | Biofluid | suitability 10; metadata 100; overall 45 | none | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE185263) | Exploratory only |
| 14 | [GSE186054](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE186054) | Transcriptomic characteristics and impaired immune function of patients with sepsis | none | Patient biofluid vs healthy control | Biofluid | suitability 10; metadata 100; overall 45 | none | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE186054) | Exploratory only |
| 15 | [GSE241238](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241238) | PBMCs from healthy volunteers or septic patients | none | Patient biofluid vs healthy control | Biofluid | suitability 10; metadata 100; overall 45 | none | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241238) | Exploratory only |
| 16 | [GSE100159](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100159) | A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring (Sepsis Datasets) | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100159) | Not suitable |
| 17 | [GSE106878](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE106878) | IFNγ/IL10 ratio stratifies corticosteroids therapy for septic shock | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE106878) | Not suitable |
| 18 | [GSE121349](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE121349) | Modulation of LTR-retrotransposons expression in mHLA-DR stratified septic shock patients: a pilot study [IS] | none | Patient biofluid vs healthy control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE121349) | Not suitable |
| 19 | [GSE13015](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13015) | Genomic Transcriptional Profiling Identifies a Blood Biomarker Signature for the Diagnosis of Septicemic Melioidosis | none | Patient biofluid vs healthy control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13015) | Not suitable |
| 20 | [GSE131761](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131761) | Gene expression patterns in septic and non-septic shock postsurgical patients | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131761) | Not suitable |
| 21 | [GSE134358](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134358) | Small non-coding RNA expression in whole blood leukocytes of healthy subjects, critically-ill patients with sepsis or non-infectious etiology and human endotoxemia | none | Treatment vs control | Biofluid | suitability 0; metadata 100; overall 34 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134358) | Not suitable |
| 22 | [GSE13736](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13736) | Gene expression of innate immune response in endothelial cells | none | Disease/model vs control | Mixed specimen/source | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13736) | Not suitable |
| 23 | [GSE13904](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13904) | Expression profiling across the pediatric systemic inflammatory response syndrome, sepsis, and septic shock spectrum | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13904) | Not suitable |
| 24 | [GSE141864](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE141864) | Extensive changes in transcriptomic “fingerprints” and immunological cells in the large organs of patients dying of acute septic shock and multiple organ failure caused by Neisseria meningitidis | none | Disease/model vs control | Tissue | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE141864) | Not suitable |
| 25 | [GSE142254](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142254) | Gene expression profiling of neutrophils from patients with cirrhosis and acute on chronic liver failure (ACLF) | none | Disease/model vs control | Unclear specimen/source | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142254) | Not suitable |
| 26 | [GSE145227](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145227) | Long noncoding RNA and messenger RNA abnormalities in pediatric sepsis | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145227) | Not suitable |
| 27 | [GSE151764](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151764) | Two distinct immunopathological profiles in lungs of lethal COVID-19 | none | Disease/model vs control | Tissue | suitability 0; metadata 100; overall 34 | MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151764) | Not suitable |
| 28 | [GSE156382](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE156382) | Neutrophil Gene expression in Acute-on-chronic liver failure (ACLF), Chronic liver disease (CLD) and Healthy Controls_AIIMSND_Aug2020 | none | Disease/model vs control | Unclear specimen/source | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE156382) | Not suitable |
| 29 | [GSE163151](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE163151) | A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE163151) | Not suitable |
| 30 | [GSE163196](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE163196) | Bulk transcriptome sequencing (bulkRNA-seq) of peripheral blood leukocytes (PBLs) in the bacterial meningitis (BM) of children | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | none | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE163196) | Not suitable |
| 31 | [GSE174507](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE174507) | Different expression of microRNAs in human sepsis | none | Patient biofluid vs healthy control | Biofluid | suitability 0; metadata 100; overall 34 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE174507) | Not suitable |
| 32 | [GSE196117](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE196117) | Transcriptional profiling of whole blood leukocytes obtained from critically ill patients with sepsis treated with clarithromycin, or not, and healthy particpants | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | none | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE196117) | Not suitable |
| 33 | [GSE224651](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE224651) | Effect of depletion of ALKBH5 on transcriptional landscape in bone marrow neutrophils from septic mice | none | Disease/model vs control | Tissue | suitability 0; metadata 100; overall 34 | SMALL_COHORT_NEEDS_REVIEW [warning]: Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review.; INTENT_ASSAY_MISMATCH [critical]: Dataset organism does not match the human patient-tissue tumor-normal intent. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE224651) | Not suitable |
| 34 | [GSE225192](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE225192) | Sepsis Induces Heterogeneous Transcription of Coagulation- and Inflammation-Associated Genes in Renal Microvasculature | none | Disease/model vs control | Tissue | suitability 0; metadata 100; overall 34 | MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [critical]: Dataset organism does not match the human patient-tissue tumor-normal intent. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE225192) | Not suitable |
| 35 | [GSE228540](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE228540) | Integrated analysis of messenger RNA and microRNA in patients with community-acquired pneumonia associated sepsis (miRNA part) | none | Patient biofluid vs healthy control | Biofluid | suitability 0; metadata 100; overall 34 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE228540) | Not suitable |
| 36 | [GSE228541](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE228541) | Integrated analysis of messenger RNA and microRNA in patients with community-acquired pneumonia associated sepsis (mRNA part) | none | Patient biofluid vs healthy control | Biofluid | suitability 0; metadata 100; overall 34 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE228541) | Not suitable |
| 37 | [GSE232753](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232753) | Bioinformatics Analysis of Gene Expression Profiles for Diagnosing Sepsis and Risk Prediction in Patients with Sepsis | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | none | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE232753) | Not suitable |
| 38 | [GSE236713](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236713) | Biomarker Validation on the ‘Analysis of geNe Expression and bioMarkers fOr poiNt-of-care dEcision support in Sepsis’ (ANEMONES) study | none | Patient biofluid vs healthy control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236713) | Not suitable |
| 39 | [GSE243217](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE243217) | Comparative Analysis of Host Responses Between Sepsis and COVID-19: A Prospective Observational Study of Whole Blood Transcriptome (RNA-Seq) | none | Patient biofluid vs healthy control | Biofluid | suitability 0; metadata 100; overall 34 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE243217) | Not suitable |
| 40 | [GSE243218](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE243218) | Comparative Analysis of Host Responses Between Sepsis and COVID-19: A Prospective Observational Study of Whole Blood Transcriptome (miRNA-Seq) | none | Patient biofluid vs healthy control | Biofluid | suitability 0; metadata 100; overall 34 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE243218) | Not suitable |
| 41 | [GSE244903](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE244903) | Detection of CD133+ cell circular RNA in sepsis patients and normal individuals | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE244903) | Not suitable |
| 42 | [GSE279448](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE279448) | Multiomics Analyses Unveil Immune Landscape in Pediatric and Adult Sepsis [bulk RNA-seq] | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | none | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE279448) | Not suitable |
| 43 | [GSE286082](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE286082) | Identifying critical lncRNAs in PBMCs linked to sepsis-induced immunosuppression using microarray analysis | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE286082) | Not suitable |
| 44 | [GSE28750](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28750) | Development and Validation of a Novel Molecular Biomarker Diagnostic Test for the Early Detection of Sepsis | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28750) | Not suitable |
| 45 | [GSE290552](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE290552) | Mapping the Molecular Signature of Progressive Multiple Sclerosis [197191] | none | Treatment vs control | Cell line | suitability 0; metadata 100; overall 34 | MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected.; CELL_LINES_INCLUDED [warning]: Cell line samples appear to be included.; TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE290552) | Not suitable |
| 46 | [GSE292448](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE292448) | RNA profiles in extracellular vesicles from severe sepsis patients reveal pathogen-specific immune signatures in meningococcal versus pneumococcal infections | none | Disease/model vs control | Extracellular vesicle | suitability 0; metadata 100; overall 34 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; EXTRACELLULAR_VESICLE_CONTEXT [warning]: Extracellular vesicle or exosome context was detected and may not represent ordinary tissue bulk RNA-seq.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE292448) | Not suitable |
| 47 | [GSE301818](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE301818) | Long non-coding RNA TTN-AS1 promotes acute liver injury in sepsis: A novel potential monitoring and therapeutic target [miRNA-Seq] | none | Patient biofluid vs healthy control | Biofluid | suitability 0; metadata 100; overall 34 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE301818) | Not suitable |
| 48 | [GSE301821](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE301821) | Long non-coding RNA TTN-AS1 promotes acute liver injury in sepsis: A novel potential monitoring and therapeutic target [RNA-Seq] | none | Disease/model vs control | Cell line | suitability 0; metadata 100; overall 34 | MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected.; CELL_LINES_INCLUDED [warning]: Cell line samples appear to be included.; SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE301821) | Not suitable |
| 49 | [GSE302306](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE302306) | Transcriptomic Profiling of CD66b+ Neutrophils from Healthy Controls and Cardiac Surgery Patients with Vasoplegic and Septic Shock Syndromes Across Multiple Timepoints | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE302306) | Not suitable |
| 50 | [GSE32707](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32707) | Inflammasome-regulated cytokines are critical mediators of lung injury in humans. | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32707) | Not suitable |
| 51 | [GSE46955](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE46955) | Transcriptome analysis of blood monocytes from sepsis patients | none | Disease/model vs control | Unclear specimen/source | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE46955) | Not suitable |
| 52 | [GSE48080](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48080) | Gene expression in peripheral mononuclear cells from septic patients secondary to community acquired pneumonia: patterns of gene expression and outcomes | none | Disease/model vs control | Unclear specimen/source | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48080) | Not suitable |
| 53 | [GSE54514](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54514) | Whole blood transcriptome of survivors and nonsurvivors of sepsis | none | Patient biofluid vs healthy control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54514) | Not suitable |
| 54 | [GSE63311](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63311) | An Endotoxin Tolerance Signature Predicts Sepsis and Organ Dysfunction at Initial Clinical Presentation | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63311) | Not suitable |
| 55 | [GSE6535](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6535) | Critically ill patients with either gram-positive sepsis or gram-negative sepsis | none | Disease/model vs control | Unclear specimen/source | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6535) | Not suitable |
| 56 | [GSE65517](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65517) | Comparative analysis of monocytes from healthy donors, patients with metastatic breast cancer, sepsis or tuberculosis. | none | Disease/model vs control | Unclear specimen/source | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65517) | Not suitable |
| 57 | [GSE65682](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65682) | Genome-wide blood transcriptional profiling in critically ill patients - MARS consortium | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65682) | Not suitable |
| 58 | [GSE66099](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66099) | Unique Patients from the Genomics of Pediatric SIRS and Septic Shock Investigators (GPSSSI) | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; THIRD_PARTY_REANALYSIS [warning]: This record is a third-party integration or reanalysis of public datasets. The GEO sample count may describe deposited atlas records rather than one independent clinical cohort; verify source-study provenance before analysis.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66099) | Not suitable |
| 59 | [GSE72326](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72326) | Modular transcriptional repertoire analyses identify neutrophil signature as candidate biomarker for lupus nephritis | none | Disease/model vs control | Mixed specimen/source | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72326) | Not suitable |
| 60 | [GSE8121](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE8121) | Pediatric septic shock | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE8121) | Not suitable |
| 61 | [GSE9692](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9692) | Validation of Genome-wide Expression patterns in Pediatric Septic Shock | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9692) | Not suitable |
| 62 | [GSE9960](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9960) | Gene-expression profiling of peripheral blood mononuclear cells in sepsis | none | Disease/model vs control | Unclear specimen/source | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9960) | Not suitable |
| 63 | [GSE104423](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104423) | Heart failure patients' peripheral blood mononuclear cell gene expression profiles before mechanical circulatory support | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104423) | Not suitable |
| 64 | [GSE10474](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10474) | Microarray Analysis of Acute Lung Injury | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10474) | Not suitable |
| 65 | [GSE110487](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110487) | Whole blood transcriptome analysis of Septic shock patients according to early therapy response | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110487) | Not suitable |
| 66 | [GSE119217](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119217) | Gene Expression Profiles in Children with Suspected Sepsis in the Emergency Department | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119217) | Not suitable |
| 67 | [GSE121350](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE121350) | Modulation of LTR-retrotransposons expression in septic shock patients: a pilot study  [MIP] | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE121350) | Not suitable |
| 68 | [GSE123729](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123729) | AKIRIN1 is a suitable reference gene in natural killer cells and granulocytes from patients with SIRS and septic shock [granulocytes] | none | Unclear study design | Unclear specimen/source | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123729) | Not suitable |
| 69 | [GSE123730](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123730) | AKIRIN1 is a suitable reference gene in natural killer cells and granulocytes from patients with SIRS and septic shock [NK cells] | none | Unclear study design | Unclear specimen/source | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123730) | Not suitable |
| 70 | [GSE12624](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12624) | Gene expression analysis in polytrauma patients comparing sepsis vs. non-sepsis | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12624) | Not suitable |
| 71 | [GSE133822](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE133822) | T cell and Monocyte Specific RNAseq Analysis in Septic and Non Septic Critically-Ill Patients and in Patients with Cancer | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE133822) | Not suitable |
| 72 | [GSE135838](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135838) | Transcriptomic Profiles of Sepsis in the Human Brain | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135838) | Not suitable |
| 73 | [GSE138712](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE138712) | Whole blood transcriptional responses of very preterm infants during late-onset sepsis | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE138712) | Not suitable |
| 74 | [GSE150707](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE150707) | IFNg Signature in Plasma Proteome Distinguishes Pediatric Hemophagocytic Lymphohistiocytosis from Sepsis and SIRS | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE150707) | Not suitable |
| 75 | [GSE157737](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157737) | Human G-MDSCs are Neutrophils at Distinct Maturation Stages that Promote Tumor Growth and Immune Cell Exclusion in Breast Cancer | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157737) | Not suitable |
| 76 | [GSE168440](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE168440) | Genomic biomarkers from urine cells indicate a unique metabolomic difference between sepsis and sterile inflammation (validation cohort) | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE168440) | Not suitable |
| 77 | [GSE168442](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE168442) | Genomic biomarkers from urine cells indicate a unique metabolomic difference between sepsis and sterile inflammation (discovery cohort) | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE168442) | Not suitable |
| 78 | [GSE180387](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE180387) | Polymorphonuclear cells show features of dysfunctional activation during fatal sepsis | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE180387) | Not suitable |
| 79 | [GSE182522](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE182522) | Using RNA-Seq to investigate immune-metabolism features in immunocompromised patients with sepsis | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE182522) | Not suitable |
| 80 | [GSE198103](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE198103) | Expression data for tumor and normal tissue samples from deceased sepsis and non-sepsis colorectal cancer patients | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE198103) | Not suitable |
| 81 | [GSE20568](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20568) | Genes associated with alcohol abuse and nicotine addiction in the human nucleus accumbens | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20568) | Not suitable |
| 82 | [GSE208581](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208581) | Risk assessment with gene expression markers in sepsis development | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208581) | Not suitable |
| 83 | [GSE208587](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208587) | Risk assessment with gene expression markers in sepsis development | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208587) | Not suitable |
| 84 | [GSE211210](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE211210) | ALKBH8 suppresses oxidative stress and ameliorates inflammation via blocking NFκB/NLRP3 axis in Sepsis | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE211210) | Not suitable |
| 85 | [GSE233322](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE233322) | lncRNA profile of whole blood cells | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE233322) | Not suitable |
| 86 | [GSE239388](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE239388) | Activation of Thousands of Genes in the Lungs and Kidneys by Sepsis is Countered by the Selective Nuclear Blockade | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; INTENT_ASSAY_MISMATCH [critical]: Dataset organism does not match the human patient-tissue tumor-normal intent.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE239388) | Not suitable |
| 87 | [GSE264050](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE264050) | Parkinson's disease (PD) genetic asymmetry in neuronal nuclei from paired hemisphere samples of prefrontal cortex | none | Unclear study design | Cell line | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected.; CELL_LINES_INCLUDED [warning]: Cell line samples appear to be included.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE264050) | Not suitable |
| 88 | [GSE282464](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE282464) | Molecular landscape of respiratory infection: A large-scale, multi-centre blood transcriptome dataset | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE282464) | Not suitable |
| 89 | [GSE296830](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE296830) | Investigation of transcriptomic signatures associated with sepsis risk in patients with infection | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE296830) | Not suitable |
| 90 | [GSE316708](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE316708) | Prolonged Loss of Oxidative Phosphorylation and Mitochondrial Mass Characterize CD66b+ Leukocytes from Patients with Sepsis | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE316708) | Not suitable |
| 91 | [GSE4607](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4607) | Systemic inflammatory response syndrome and septic shock | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4607) | Not suitable |
| 92 | [GSE5262](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5262) | Septic shock patients: outcome at D1 (24 hours after inclusion) | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5262) | Not suitable |
| 93 | [GSE5271](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5271) | Time evolution study of sepsis in patients at D1, D7 and D28 post-inclusion | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5271) | Not suitable |
| 94 | [GSE63042](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63042) | An integrated transcriptome and expressed variant analysis of sepsis survival and death | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63042) | Not suitable |
| 95 | [GSE64498](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE64498) | Gene expression comparison of post-sepsis versus naïve mice-derived tumor associated macrophages | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [critical]: Dataset organism does not match the human patient-tissue tumor-normal intent.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE64498) | Not suitable |
| 96 | [GSE66890](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66890) | Expression of Neutrophil-related genes in patients with early sepsis-induced ARDS | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66890) | Not suitable |
| 97 | [GSE69528](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE69528) | A Blood Transcriptional Diagnostic Assay for Septicemic Melioidosis | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE69528) | Not suitable |
| 98 | [GSE69686](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE69686) | Post-natal age is a critical determinant of the neonatal host response to sepsis | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE69686) | Not suitable |
| 99 | [GSE70311](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70311) | Transcriptomic profiling of the inflammatory response after trauma | none | Unclear study design | Unclear specimen/source | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70311) | Not suitable |
| 100 | [GSE70461](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70461) | Gene expression profiles in preterm infants on continuous long-term oxygen therapy suggest reduced oxidative stress-dependent signaling during hypoxia | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70461) | Not suitable |
| 101 | [GSE74224](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE74224) | Discrimination of SIRS from Sepsis in Critically Ill Adults | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE74224) | Not suitable |
| 102 | [GSE84439](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84439) | Whole blood RNA sequencing in idiopathic pneumonia syndrome reveals a unique transcriptomic profile compared to ARDS | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84439) | Not suitable |
| 103 | [GSE94717](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE94717) | Differentially expressed miRNAs in sepsis-induced acute kidney injury target oxidative stress and mitochondrial dysfunction pathways | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE94717) | Not suitable |
| 104 | [GSE101639](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101639) | Circulating microRNA expression patterns and target prediction in sepsis development | none | Patient biofluid vs healthy control | Biofluid | suitability 0; metadata 85; overall 34 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101639) | Not suitable |
| 105 | [GSE13205](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13205) | Skeletal muscle transcriptome in ICU patients suffering from sepsis induced multiple organ failure | none | Disease/model vs control | Unclear specimen/source | suitability 0; metadata 85; overall 34 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13205) | Not suitable |
| 106 | [GSE149764](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE149764) | small RNA sequencing of plasma miRNA from sepsis patients | none | Patient biofluid vs healthy control | Biofluid | suitability 0; metadata 85; overall 34 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE149764) | Not suitable |
| 107 | [GSE184803](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE184803) | Plasma extracellular vesicle miR-483-3p and let-7d-3p as potential biomarkers for sepsis | none | Disease/model vs control | Extracellular vesicle | suitability 0; metadata 85; overall 34 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; EXTRACELLULAR_VESICLE_CONTEXT [warning]: Extracellular vesicle or exosome context was detected and may not represent ordinary tissue bulk RNA-seq.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE184803) | Not suitable |
| 108 | [GSE210797](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE210797) | A Role for IFITM3 in Regulating Fibrinogen Endocytosis and Platelet Reactivity in Non-Viral Sepsis | none | Disease/model vs control | Tissue | suitability 0; metadata 85; overall 34 | none | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE210797) | Not suitable |
| 109 | [GSE252275](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE252275) | Gene expression analysis in platelets of septic patients | none | Disease/model vs control | Tissue | suitability 0; metadata 85; overall 34 | MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE252275) | Not suitable |
| 110 | [GSE294059](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294059) | RNA-seq of PBMCs of patients with sepsis and nonseptic controls | none | Disease/model vs control | Biofluid | suitability 0; metadata 85; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294059) | Not suitable |
| 111 | [GSE310375](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE310375) | β-Nicotinamide mononucleotide restores mitochondrial function and muscle strength in septic male mice | none | Disease/model vs control | Tissue | suitability 0; metadata 85; overall 34 | INTENT_ASSAY_MISMATCH [critical]: Dataset organism does not match the human patient-tissue tumor-normal intent. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE310375) | Not suitable |
| 112 | [GSE5772](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5772) | Leukocytes from patients with sepsis | none | Disease/model vs control | Unclear specimen/source | suitability 0; metadata 85; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5772) | Not suitable |
| 113 | [GSE89376](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE89376) | Insights into the function of long noncoding RNAs in sepsis revealed by gene co-expression network analysis | none | Disease/model vs control | Unclear specimen/source | suitability 0; metadata 85; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE89376) | Not suitable |
| 114 | [GSE137341](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137341) | Blood transcriptome of human sepsis in an Indian cohort [Affymetrix array] | none | Unclear study design | Biofluid | suitability 0; metadata 83; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; TECHNICAL_REPLICATES_DETECTED [warning]: Technical replicate samples were detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137341) | Not suitable |
| 115 | [GSE139913](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE139913) | Differential gene expression in circulating CD14+ monocytes indicates the prognosis of critically ill patients with sepsis | none | Unclear study design | Unclear specimen/source | suitability 0; metadata 78; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE139913) | Not suitable |
| 116 | [GSE218494](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE218494) | Altered gene expression in plasma of patients with pneumonia-induced sepsis compared to pneumonia without sepsis and healthy people | none | Unclear study design | Biofluid | suitability 0; metadata 78; overall 34 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE218494) | Not suitable |
| 117 | [GSE267399](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE267399) | Critical Role of MALAT1 in Gram-negative Bacteria-induced Coagulation via regulating GSDMD-dependent TF activity | none | Unclear study design | Unclear specimen/source | suitability 0; metadata 78; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE267399) | Not suitable |
| 118 | [GSE79962](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE79962) | Widespread downregulation of cardiac mitochondrial and sarcomeric genes in patients with sepsis | none | Unclear study design | Tissue | suitability 0; metadata 78; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE79962) | Not suitable |
| 119 | [GSE82315](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE82315) | Expression data from human monocytes stimulated with wild-type N. meningitidis and recombinant IL-10 [II] | none | Unclear study design | Biofluid | suitability 0; metadata 78; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE82315) | Not suitable |
| 120 | [GSE67652](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67652) | Septic shock in advanced age: Transcriptome analysis reveals altered molecular signatures in neutrophil granulocytes | none | Unclear study design | Unclear specimen/source | suitability 0; metadata 70; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67652) | Not suitable |

## Ranking explanations

### GSE142255

Dataset can inform exploration but is not strong enough for primary analysis.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 20%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis, Septic shock.
- Processed data is available for downstream review.
- External evidence: PubMed links 4 publications; 4 DOIs available: PMID 33613548, PMID 35982134, PMID 37478215, PMID 40070835.
- Publication context: Characterization of Blood Immune Cells in Patients With Decompensated Cirrhosis Including ACLF.. Frontiers in immunology, 2020. PMID 33613548. DOI 10.3389/fimmu.2020.619039.
- Publication context: Bioinformatics analyses of potential ACLF biological mechanisms and identification of immune-related hub genes and vital miRNAs.. Scientific reports, 2022. PMID 35982134. DOI 10.1038/s41598-022-18396-1.
- Publication context: CD3D and CD247 are the molecular targets of septic shock.. Medicine, 2023. PMID 37478215. DOI 10.1097/MD.0000000000034295.
- Publication context: 1 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: patient with stable cirrhosis vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Exploratory only: Dataset can inform exploration but is not strong enough for primary analysis.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE205672

Dataset can inform exploration but is not strong enough for primary analysis.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 20%.
- Downgraded for tissue search because it is a biofluid cohort.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Exploratory only: Dataset can inform exploration but is not strong enough for primary analysis.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.

### GSE208092

Dataset can inform exploration but is not strong enough for primary analysis.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 20%.
- Downgraded for tissue search because it is a biofluid cohort.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: COVID-19, Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Exploratory only: Dataset can inform exploration but is not strong enough for primary analysis.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 

### GSE217700

Dataset can inform exploration but is not strong enough for primary analysis.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 20%.
- Downgraded for tissue search because it is a biofluid cohort.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Infectious disease or host response, Sepsis, Systemic inflammatory response syndrome.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because fewer than ten samples limit cohort confidence.
- DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence.
- RECOMMENDATION_REASON: Exploratory only: Dataset can inform exploration but is not strong enough for primary analysis.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 

### GSE26378

Dataset can inform exploration but is not strong enough for primary analysis.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 20%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Septic shock.
- Processed data is available for downstream review.
- External evidence: PubMed links 23 publications; 23 DOIs available: PMID 21738952, PMID 24650276, PMID 26376786, PMID 32575108, PMID 35082520.
- Publication context: The influence of developmental age on the early transcriptomic response of children with septic shock.. Molecular medicine (Cambridge, Mass.), 2011. PMID 21738952. DOI 10.2119/molmed.2011.00169.
- Publication context: Corticosteroids are associated with repression of adaptive immunity gene programs in pediatric septic shock.. American journal of respiratory and critical care medicine, 2014. PMID 24650276. DOI 10.1164/rccm.201401-0171OC.
- Publication context: Differential expression of the Nrf2-linked genes in pediatric septic shock.. Critical care (London, England), 2015. PMID 26376786. DOI 10.1186/s13054-015-1052-0.
- Publication context: 20 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Exploratory only: Dataset can inform exploration but is not strong enough for primary analysis.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE26440

Dataset can inform exploration but is not strong enough for primary analysis.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 20%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Septic shock.
- Processed data is available for downstream review.
- External evidence: PubMed links 24 publications; 24 DOIs available: PMID 19624809, PMID 21738952, PMID 24650276, PMID 26376786, PMID 39315170.
- Publication context: Identification of pediatric septic shock subclasses based on genome-wide expression profiling.. BMC medicine, 2009. PMID 19624809. DOI 10.1186/1741-7015-7-34.
- Publication context: The influence of developmental age on the early transcriptomic response of children with septic shock.. Molecular medicine (Cambridge, Mass.), 2011. PMID 21738952. DOI 10.2119/molmed.2011.00169.
- Publication context: Corticosteroids are associated with repression of adaptive immunity gene programs in pediatric septic shock.. American journal of respiratory and critical care medicine, 2014. PMID 24650276. DOI 10.1164/rccm.201401-0171OC.
- Publication context: 21 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Exploratory only: Dataset can inform exploration but is not strong enough for primary analysis.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: AMBIGUOUS_SAMPLES_DETECTED [info]: Ambiguous sample metadata was detected in 32 sample(s): GSM648630 matched "group: n/a"; GSM648631 matched "group: n/a"; GSM648632 matched "group: n/a"; additional ambiguous samples omitted. Review these samples before inclusion or manual group assignment.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- AMBIGUOUS_SAMPLES_DETECTED [INFO]: Ambiguous sample metadata was detected in 32 sample(s): GSM648630 matched "group: n/a"; GSM648631 matched "group: n/a"; GSM648632 matched "group: n/a"; additional ambiguous samples omitted. Review these samples before inclusion or manual group assignment.; samples: GSM648630, GSM648631, GSM648632, GSM648637, GSM648638, GSM648639, GSM648640, GSM648641, GSM648668, GSM648669, GSM648671, GSM648672, GSM648673, GSM648674, GSM648676, GSM648677, GSM648678, GSM648679, GSM648681, GSM648686, GSM648687, GSM648688, GSM648689, GSM648690, GSM648691, GSM648692, GSM648693, GSM648694, GSM648699, GSM648700, GSM648701, GSM648703
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE294985

Dataset can inform exploration but is not strong enough for primary analysis.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 20%.
- Downgraded for tissue search because it is a biofluid cohort.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Infectious disease or host response, Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 41783141.
- Publication context: Construction of a robust sepsis prognostic classifier based on E3 ubiquitin ligase-related genes.. Frontiers in molecular biosciences, 2026. PMID 41783141. DOI 10.3389/fmolb.2026.1726356.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Exploratory only: Dataset can inform exploration but is not strong enough for primary analysis.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.

### GSE60424

Dataset can inform exploration but is not strong enough for primary analysis.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 20%.
- Downgraded for tissue search because it is a biofluid cohort.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Amyotrophic lateral sclerosis, Metabolic disease, Sepsis, Type 1 diabetes.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: type 1 diabetes vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Exploratory only: Dataset can inform exploration but is not strong enough for primary analysis.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.

### GSE69063

Dataset can inform exploration but is not strong enough for primary analysis.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 20%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 9 publications; 9 DOIs available: PMID 34228845, PMID 36583159, PMID 37469874, PMID 37662976, PMID 38628767.
- Publication context: Small nucleolar RNA networks are up-regulated during human anaphylaxis.. Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology, 2021. PMID 34228845. DOI 10.1111/cea.13982.
- Publication context: Genes involved in platelet aggregation and activation are downregulated during acute anaphylaxis in humans.. Clinical & translational immunology, 2022. PMID 36583159. DOI 10.1002/cti2.1435.
- Publication context: Identification of the biological processes, immune cell landscape, and hub genes shared by acute anaphylaxis and ST-segment elevation myocardial infarction.. Frontiers in pharmacology, 2023. PMID 37469874. DOI 10.3389/fphar.2023.1211332.
- Publication context: 6 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: anaphylaxis vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Exploratory only: Dataset can inform exploration but is not strong enough for primary analysis.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE80496

Dataset can inform exploration but is not strong enough for primary analysis.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 20%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 3 publications; 3 DOIs available: PMID 27552617, PMID 41007866, PMID 42286943.
- Publication context: Diagnostic Test Accuracy of a 2-Transcript Host RNA Signature for Discriminating Bacterial vs Viral Infection in Febrile Children.. JAMA, 2016. PMID 27552617. DOI 10.1001/jama.2016.11236.
- Publication context: Key Common Genes with LTF and MMP9 Between Sepsis and Relapsed B-Cell Lineage Acute Lymphoblastic Leukemia in Children.. Biomedicines, 2025. PMID 41007866. DOI 10.3390/biomedicines13092307.
- Publication context: Lactate-Associated Gene Signatures as Predictors: A Comprehensive Analysis of Immune Profiles in Sepsis.. Journal of intensive care medicine, 2026. PMID 42286943. DOI 10.1177/08850666261458765.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Exploratory only: Dataset can inform exploration but is not strong enough for primary analysis.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE134347

Dataset can inform exploration but is not strong enough for primary analysis.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 10%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 20 publications; 20 DOIs available: PMID 33305733, PMID 35401666, PMID 35787932, PMID 35903199, PMID 36765335.
- Publication context: The leukocyte non-coding RNA landscape in critically ill patients with sepsis.. eLife, 2020. PMID 33305733. DOI 10.7554/eLife.58597.
- Publication context: Identification of Hub Genes With Differential Correlations in Sepsis.. Frontiers in genetics, 2022. PMID 35401666. DOI 10.3389/fgene.2022.876514.
- Publication context: Contribution of prognostic ferroptosis-related subtypes classification and hub genes of sepsis.. Transplant immunology, 2022. PMID 35787932. DOI 10.1016/j.trim.2022.101660.
- Publication context: 17 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Exploratory only: Dataset can inform exploration but is not strong enough for primary analysis.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE137340

Dataset can inform exploration but is not strong enough for primary analysis.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 10%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis, Septic shock, Severe sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 4 publications; 4 DOIs available: PMID 38363924, PMID 39586719, PMID 40129981, PMID 41947789.
- Publication context: LCN2 and ELANE overexpression induces sepsis.. Medicine, 2024. PMID 38363924. DOI 10.1097/MD.0000000000037255.
- Publication context: [Exploration of key ferroptosis-related genes as therapeutic targets for sepsis based on bioinformatics and the depiction of their immune profiles characterization].. Zhonghua wei zhong bing ji jiu yi xue, 2024. PMID 39586719. DOI 10.3760/cma.j.cn121430-20240524-00457.
- Publication context: Comprehensive integration of diagnostic biomarker analysis and immune cell infiltration features in sepsis via machine learning and bioinformatics techniques.. Frontiers in immunology, 2025. PMID 40129981. DOI 10.3389/fimmu.2025.1526174.
- Publication context: 1 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Exploratory only: Dataset can inform exploration but is not strong enough for primary analysis.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: AMBIGUOUS_SAMPLES_DETECTED [info]: Ambiguous sample metadata was detected in 2 sample(s): GSM4075803 matched "diagnosis: NA"; GSM4075804 matched "diagnosis: NA". Review these samples before inclusion or manual group assignment.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- AMBIGUOUS_SAMPLES_DETECTED [INFO]: Ambiguous sample metadata was detected in 2 sample(s): GSM4075803 matched "diagnosis: NA"; GSM4075804 matched "diagnosis: NA". Review these samples before inclusion or manual group assignment.; samples: GSM4075803, GSM4075804
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE185263

Dataset can inform exploration but is not strong enough for primary analysis.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 10%.
- Downgraded for tissue search because it is a biofluid cohort.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 14 publications; 13 DOIs available: PMID 35027333, PMID 36250055, PMID 36690713, PMID 36920635, PMID 37090709.
- Publication context: Predicting sepsis severity at first clinical presentation: The role of endotypes and mechanistic signatures.. EBioMedicine, 2022. PMID 35027333. DOI 10.1016/j.ebiom.2021.103776.
- Publication context: Significant difference of differential expression pyroptosis-related genes and their correlations with infiltrated immune cells in sepsis.. Frontiers in cellular and infection microbiology, 2022. PMID 36250055. DOI 10.3389/fcimb.2022.1005392.
- Publication context: Predicting severity in COVID-19 disease using sepsis blood gene expression signatures.. Scientific reports, 2023. PMID 36690713. DOI 10.1038/s41598-023-28259-y.
- Publication context: 11 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Exploratory only: Dataset can inform exploration but is not strong enough for primary analysis.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.

### GSE186054

Dataset can inform exploration but is not strong enough for primary analysis.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 10%.
- Downgraded for tissue search because it is a biofluid cohort.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Infectious disease or host response, Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because fewer than ten samples limit cohort confidence.
- DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence.
- RECOMMENDATION_REASON: Exploratory only: Dataset can inform exploration but is not strong enough for primary analysis.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.

### GSE241238

Dataset can inform exploration but is not strong enough for primary analysis.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 10%.
- Downgraded for tissue search because it is a biofluid cohort.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 42143071.
- Publication context: LncRNA TUG1 mitigates sepsis-induced acute lung injury via a ceRNA network regulating the CALM1/PRKG1/RYR3/AQP5 axis.. Scientific reports, 2026. PMID 42143071. DOI 10.1038/s41598-026-51003-1.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because fewer than ten samples limit cohort confidence.
- DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence.
- RECOMMENDATION_REASON: Exploratory only: Dataset can inform exploration but is not strong enough for primary analysis.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.

### GSE100159

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 9 publications; 9 DOIs available: PMID 32736569, PMID 33377660, PMID 34282143, PMID 36918848, PMID 37845713.
- Publication context: A modular framework for the development of targeted Covid-19 blood transcript profiling panels.. Journal of translational medicine, 2020. PMID 32736569. DOI 10.1186/s12967-020-02456-z.
- Publication context: Definition of erythroid cell-positive blood transcriptome phenotypes associated with severe respiratory syncytial virus infection.. Clinical and translational medicine, 2020. PMID 33377660. DOI 10.1002/ctm2.244.
- Publication context: Development of a fixed module repertoire for the analysis and interpretation of blood transcriptome data.. Nature communications, 2021. PMID 34282143. DOI 10.1038/s41467-021-24584-w.
- Publication context: 6 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE106878

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis, Septic shock, Severe sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 38054005.
- Publication context: A simplified machine learning model utilizing platelet-related genes for predicting poor prognosis in sepsis.. Frontiers in immunology, 2023. PMID 38054005. DOI 10.3389/fimmu.2023.1286203.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: septic shock vs vehicle control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE121349

Dataset does not meet the current suitability threshold.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis, Septic shock.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 32188504.
- Publication context: Dynamic LTR retrotransposon transcriptome landscape in septic shock patients.. Critical care (London, England), 2020. PMID 32188504. DOI 10.1186/s13054-020-2788-8.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: septic shock vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE13015

Dataset does not meet the current suitability threshold.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Metabolic disease, Sepsis, Type 2 diabetes.
- Processed data is available for downstream review.
- External evidence: PubMed links 3 publications; 3 DOIs available: PMID 19903332, PMID 33624743, PMID 35223539.
- Publication context: Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis.. Genome biology, 2009. PMID 19903332. DOI 10.1186/gb-2009-10-11-r127.
- Publication context: BloodGen3Module: blood transcriptional module repertoire analysis and visualization using R.. Bioinformatics (Oxford, England), 2021. PMID 33624743. DOI 10.1093/bioinformatics/btab121.
- Publication context: Differential Gene Sets Profiling in Gram-Negative and Gram-Positive Sepsis.. Frontiers in cellular and infection microbiology, 2022. PMID 35223539. DOI 10.3389/fcimb.2022.801232.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE131761

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis, Septic shock, Systemic inflammatory response syndrome.
- Processed data is available for downstream review.
- External evidence: PubMed links 21 publications; 21 DOIs available: PMID 34144116, PMID 35345523, PMID 35971090, PMID 36506322, PMID 37164163.
- Publication context: Distinguishing septic shock from non-septic shock in postsurgical patients using gene expression.. The Journal of infection, 2021. PMID 34144116. DOI 10.1016/j.jinf.2021.05.039.
- Publication context: Identification of Nine mRNA Signatures for Sepsis Using Random Forest.. Computational and mathematical methods in medicine, 2022. PMID 35345523. DOI 10.1155/2022/5650024.
- Publication context: Multiple datasets to explore the molecular mechanism of sepsis.. BMC genomic data, 2022. PMID 35971090. DOI 10.1186/s12863-022-01078-2.
- Publication context: 18 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE134358

Dataset does not meet the current suitability threshold.

- Comparison: Treatment vs control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because it is a treatment/control experiment.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Endotoxemia, Infectious disease or host response, Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 2 publications; 2 DOIs available: PMID 33305733, PMID 37701780.
- Publication context: The leukocyte non-coding RNA landscape in critically ill patients with sepsis.. eLife, 2020. PMID 33305733. DOI 10.7554/eLife.58597.
- Publication context: Diagnostic and prognostic value of autophagy-related key genes in sepsis and potential correlation with immune cell signatures.. Frontiers in cell and developmental biology, 2023. PMID 37701780. DOI 10.3389/fcell.2023.1218379.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: noninfectious vs mixed controls.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons.
- DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- COMPARISON_SUITABILITY: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- DOWNGRADE_REASON: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE13736

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Mixed specimen/source. Comparison suitability: 0%.
- Downgraded for tissue search because specimen/source classes are mixed.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Metabolic disease, Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 19845532.
- Publication context: Staphylococcus aureus isolates from blood and anterior nares induce similar innate immune responses in endothelial cells.. APMIS : acta pathologica, microbiologica, et immunologica Scandinavica, 2009. PMID 19845532. DOI 10.1111/j.1600-0463.2009.02535.x.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Mixed specimen/source dataset downgraded until tissue samples are clearly separated.
- DOWNGRADE_REASON: Mixed specimen/source dataset downgraded until tissue samples are clearly separated.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because specimen/source classes are mixed.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: 

### GSE13904

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis, Septic shock, Systemic inflammatory response syndrome.
- Processed data is available for downstream review.
- External evidence: PubMed links 21 publications; 21 DOIs available: PMID 19325468, PMID 38795170, PMID 38894720, PMID 39315170, PMID 39578562.
- Publication context: Genomic expression profiling across the pediatric systemic inflammatory response syndrome, sepsis, and septic shock spectrum.. Critical care medicine, 2009. PMID 19325468. DOI 10.1097/CCM.0b013e31819fcc08.
- Publication context: Screening and Identification of Neutrophil Extracellular Trap-related Diagnostic Biomarkers for Pediatric Sepsis by Machine Learning.. Inflammation, 2025. PMID 38795170. DOI 10.1007/s10753-024-02059-6.
- Publication context: Identification of apoptosis-immune-related gene signature and construction of diagnostic model for sepsis based on single-cell sequencing and bulk transcriptome analysis.. Frontiers in genetics, 2024. PMID 38894720. DOI 10.3389/fgene.2024.1389630.
- Publication context: 18 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE141864

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Septic shock.
- Processed data is available for downstream review.
- External evidence: PubMed links 3 publications; 3 DOIs available: PMID 32154187, PMID 37553892, PMID 40271227.
- Publication context: Extensive Changes in Transcriptomic "Fingerprints" and Immunological Cells in the Large Organs of Patients Dying of Acute Septic Shock and Multiple Organ Failure Caused by Neisseria meningitidis.. Frontiers in cellular and infection microbiology, 2020. PMID 32154187. DOI 10.3389/fcimb.2020.00042.
- Publication context: A TRANSCRIPTOMIC APPRECIATION OF CHILDHOOD MENINGOCOCCAL AND POLYMICROBIAL SEPSIS FROM A PRO-INFLAMMATORY AND TRAJECTORIAL PERSPECTIVE, A ROLE FOR VASCULAR ENDOTHELIAL GROWTH FACTOR A AND B MODULATION?. Shock (Augusta, Ga.), 2023. PMID 37553892. DOI 10.1097/SHK.0000000000002192.
- Publication context: Validation of Senescence of the Role of ATM/P53 Pathway in Myocardial Senescence in Mice with Sepsis.. Infection and drug resistance, 2025. PMID 40271227. DOI 10.2147/IDR.S505836.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: septic shock vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE142254

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 33613548.
- Publication context: Characterization of Blood Immune Cells in Patients With Decompensated Cirrhosis Including ACLF.. Frontiers in immunology, 2020. PMID 33613548. DOI 10.3389/fimmu.2020.619039.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: patient with stable cirrhosis vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: 

### GSE145227

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 6 publications; 6 DOIs available: PMID 32151258, PMID 34053485, PMID 35444449, PMID 37901228, PMID 37921181.
- Publication context: Long noncoding RNA and messenger RNA abnormalities in pediatric sepsis: a preliminary study.. BMC medical genomics, 2020. PMID 32151258. DOI 10.1186/s12920-020-0698-x.
- Publication context: [Construction of sepsis-associated competing endogenous RNA network based on Gene Expression Omnibus datasets and bioinformatic analysis].. Zhonghua wei zhong bing ji jiu yi xue, 2021. PMID 34053485. DOI 10.3760/cma.j.cn121430-20210205-00211.
- Publication context: Identification of Immune-Related Key Genes as Potential Diagnostic Biomarkers of Sepsis in Children.. Journal of inflammation research, 2022. PMID 35444449. DOI 10.2147/JIR.S359908.
- Publication context: 3 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE151764

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: COVID-19, Fibrosis, Infectious disease or host response, Metabolic disease, Sepsis, Tuberculosis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: tumor sample vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 

### GSE156382

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 2 publications; 2 DOIs available: PMID 34552111, PMID 40070835.
- Publication context: Inflammatory signature in acute-on-chronic liver failure includes increased expression of granulocyte genes ELANE, MPO and CD177.. Scientific reports, 2021. PMID 34552111. DOI 10.1038/s41598-021-98086-6.
- Publication context: Identification and validation of neutrophil-related biomarkers in acute-on-chronic liver failure.. Frontiers in immunology, 2025. PMID 40070835. DOI 10.3389/fimmu.2025.1477342.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: 

### GSE163151

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: COVID-19, Infectious disease or host response, Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 6 publications; 6 DOIs available: PMID 33536218, PMID 34730223, PMID 34880855, PMID 37533853, PMID 37991568.
- Publication context: A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood.. Science advances, 2021. PMID 33536218. DOI 10.1126/sciadv.abe5984.
- Publication context: Identification of hub genes and molecular subtypes in COVID-19 based on WGCNA.. European review for medical and pharmacological sciences, 2021. PMID 34730223. DOI 10.26355/eurrev_202110_27015.
- Publication context: Transcriptional Profiling and Machine Learning Unveil a Concordant Biosignature of Type I Interferon-Inducible Host Response Across Nasal Swab and Pulmonary Tissue for COVID-19 Diagnosis.. Frontiers in immunology, 2021. PMID 34880855. DOI 10.3389/fimmu.2021.733171.
- Publication context: 3 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: viral acute respiratory illness vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 

### GSE163196

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs normal tissue.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.

### GSE174507

Dataset does not meet the current suitability threshold.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 36102304.
- Publication context: MicroRNAs combined with the TLR4/TDAG8 mRNAs and proinflammatory cytokines are biomarkers for the rapid diagnosis of sepsis.. Molecular medicine reports, 2022. PMID 36102304. DOI 10.3892/mmr.2022.12850.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- DOWNGRADE_REASON: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
- DOWNGRADE_REASON: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE196117

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.

### GSE224651

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Infectious disease or host response, Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 38114747.
- Publication context: The RNA m(6)A demethylase ALKBH5 drives emergency granulopoiesis and neutrophil mobilization by upregulating G-CSFR expression.. Cellular & molecular immunology, 2024. PMID 38114747. DOI 10.1038/s41423-023-01115-9.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because non-human datasets are outside the selected human ranking intent.
- DOWNGRADE_REASON: Overall score capped because non-human datasets are outside the selected human ranking intent.
- OVERALL: Overall score capped because fewer than six samples are too small for top-ranked cohort confidence.
- DOWNGRADE_REASON: Overall score capped because fewer than six samples are too small for top-ranked cohort confidence.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- WARNING_CODE: SMALL_COHORT_NEEDS_REVIEW [warning]: Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [critical]: Dataset organism does not match the human patient-tissue tumor-normal intent.
- SMALL_COHORT_NEEDS_REVIEW [WARNING]: Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review.; samples: 
- INTENT_ASSAY_MISMATCH [CRITICAL]: Dataset organism does not match the human patient-tissue tumor-normal intent.; samples: 

### GSE225192

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 40369453.
- Publication context: Neutrophil extracellular traps-related genes contribute to sepsis-associated acute kidney injury.. BMC nephrology, 2025. PMID 40369453. DOI 10.1186/s12882-025-04126-y.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sham-operated vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because non-human datasets are outside the selected human ranking intent.
- DOWNGRADE_REASON: Overall score capped because non-human datasets are outside the selected human ranking intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [critical]: Dataset organism does not match the human patient-tissue tumor-normal intent.
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [CRITICAL]: Dataset organism does not match the human patient-tissue tumor-normal intent.; samples: 

### GSE228540

Dataset does not meet the current suitability threshold.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Infectious disease or host response, Sepsis, Septic shock, Severe sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- DOWNGRADE_REASON: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
- DOWNGRADE_REASON: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 

### GSE228541

Dataset does not meet the current suitability threshold.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Infectious disease or host response, Sepsis, Septic shock, Severe sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- DOWNGRADE_REASON: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
- DOWNGRADE_REASON: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 

### GSE232753

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 3 publications; 3 DOIs available: PMID 37298316, PMID 40056630, PMID 40318009.
- Publication context: Bioinformatics Analysis of Gene Expression Profiles for Diagnosing Sepsis and Risk Prediction in Patients with Sepsis.. International journal of molecular sciences, 2023. PMID 37298316. DOI 10.3390/ijms24119362.
- Publication context: Neutrophil-derived exosomal S100A8 aggravates lung injury in sepsis by inducing pyroptosis.. Molecular immunology, 2025. PMID 40056630. DOI 10.1016/j.molimm.2025.03.003.
- Publication context: Identification and Verification of Necroptosis-Related Genes in Patients With Sepsis by Bioinformatic Analysis and Molecular Experiments.. Journal of cellular and molecular medicine, 2025. PMID 40318009. DOI 10.1111/jcmm.70582.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.

### GSE236713

Dataset does not meet the current suitability threshold.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis, Systemic inflammatory response syndrome.
- Processed data is available for downstream review.
- External evidence: PubMed links 5 publications; 5 DOIs available: PMID 38332914, PMID 40129981, PMID 40909263, PMID 41570698, PMID 42291298.
- Publication context: The 'analysis of gene expression and biomarkers for point-of-care decision support in Sepsis' study; temporal clinical parameter analysis and validation of early diagnostic biomarker signatures for severe inflammation andsepsis-SIRS discrimination.. Frontiers in immunology, 2023. PMID 38332914. DOI 10.3389/fimmu.2023.1308530.
- Publication context: Comprehensive integration of diagnostic biomarker analysis and immune cell infiltration features in sepsis via machine learning and bioinformatics techniques.. Frontiers in immunology, 2025. PMID 40129981. DOI 10.3389/fimmu.2025.1526174.
- Publication context: Identification of sepsis biomarkers through glutamine metabolism-mediated immune regulation: a comprehensive analysis employing mendelian randomization, multi-omics integration, and machine learning.. Frontiers in immunology, 2025. PMID 40909263. DOI 10.3389/fimmu.2025.1640425.
- Publication context: 2 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE243217

Dataset does not meet the current suitability threshold.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: COVID-19, Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 39160575.
- Publication context: Bacterial sepsis causes more dramatic pathogenetic changes in the Th1 pathway than does viral (COVID-19) sepsis: a prospective observational study of whole blood transcriptomes.. Virology journal, 2024. PMID 39160575. DOI 10.1186/s12985-024-02451-6.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: COVID-19 vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- DOWNGRADE_REASON: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
- DOWNGRADE_REASON: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 

### GSE243218

Dataset does not meet the current suitability threshold.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: COVID-19, Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: COVID-19 vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- DOWNGRADE_REASON: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
- DOWNGRADE_REASON: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 

### GSE244903

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 39071490.
- Publication context: Circular RNAs as potential biomarkers for male severe sepsis.. Open life sciences, 2024. PMID 39071490. DOI 10.1515/biol-2022-0900.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- DOWNGRADE_REASON: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because fewer than ten samples limit cohort confidence.
- DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence.
- OVERALL: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
- DOWNGRADE_REASON: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE279448

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Infectious disease or host response, Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis vs mixed controls.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.

### GSE286082

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 40189572.
- Publication context: Identification of lncRNAs in peripheral blood mononuclear cells associated with sepsis immunosuppression based on weighted gene co-expression network analysis.. Hereditas, 2025. PMID 40189572. DOI 10.1186/s41065-025-00400-z.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because fewer than ten samples limit cohort confidence.
- DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE28750

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis, Systemic inflammatory response syndrome.
- Processed data is available for downstream review.
- External evidence: PubMed links 21 publications; 21 DOIs available: PMID 21682927, PMID 39586719, PMID 39654893, PMID 40129981, PMID 40201575.
- Publication context: Development and validation of a novel molecular biomarker diagnostic test for the early detection of sepsis.. Critical care (London, England), 2011. PMID 21682927. DOI 10.1186/cc10274.
- Publication context: [Exploration of key ferroptosis-related genes as therapeutic targets for sepsis based on bioinformatics and the depiction of their immune profiles characterization].. Zhonghua wei zhong bing ji jiu yi xue, 2024. PMID 39586719. DOI 10.3760/cma.j.cn121430-20240524-00457.
- Publication context: IL7R, GZMA and CD8A serve as potential molecular biomarkers for sepsis based on bioinformatics analysis.. Frontiers in immunology, 2024. PMID 39654893. DOI 10.3389/fimmu.2024.1445858.
- Publication context: 18 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE290552

Dataset does not meet the current suitability threshold.

- Comparison: Treatment vs control. Specimen: Cell line. Comparison suitability: 0%.
- Downgraded for tissue search because it is a model-system experiment.
- Downgraded for tissue search because it is a treatment/control experiment.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Infectious disease or host response, Neurodegeneration, Pancreatic cancer, Prostate cancer, Rheumatoid arthritis, Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: stimulated vs control.
- COMPARISON_SUITABILITY: Excluded sample type flags reduce suitability.
- DOWNGRADE_REASON: Excluded sample type flags reduce suitability.
- COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons.
- DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons.
- COMPARISON_SUITABILITY: Organoid or cell-line experiment downgraded for patient tissue search intent.
- DOWNGRADE_REASON: Organoid or cell-line experiment downgraded for patient tissue search intent.
- COMPARISON_SUITABILITY: Excluded model-system sample markers reduce suitability.
- DOWNGRADE_REASON: Excluded model-system sample markers reduce suitability.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a model-system experiment.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment.
- WARNING_CODE: MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected.
- WARNING_CODE: CELL_LINES_INCLUDED [warning]: Cell line samples appear to be included.
- WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.
- MIXED_SAMPLE_TYPES [WARNING]: Multiple sample type labels or exclusion flags were detected.; samples: 
- CELL_LINES_INCLUDED [WARNING]: Cell line samples appear to be included.; samples: GSM8816432, GSM8816433, GSM8816434, GSM8816435, GSM8816436, GSM8816437, GSM8816438, GSM8816439, GSM8816440, GSM8816441, GSM8816442, GSM8816443, GSM8816444, GSM8816445, GSM8816446, GSM8816447
- TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM8816432, GSM8816433, GSM8816434, GSM8816435, GSM8816436, GSM8816437, GSM8816438, GSM8816439, GSM8816440, GSM8816441, GSM8816442, GSM8816443, GSM8816444, GSM8816445, GSM8816446, GSM8816447

### GSE292448

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Extracellular vesicle. Comparison suitability: 0%.
- Downgraded for tissue search because it is an extracellular-vesicle or exosome dataset.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis, Septic shock, Severe sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: systemic pneumococcal disease (spd) patient vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Extracellular-vesicle or exosome dataset downgraded because this ranking targets ordinary tissue bulk RNA-seq.
- DOWNGRADE_REASON: Extracellular-vesicle or exosome dataset downgraded because this ranking targets ordinary tissue bulk RNA-seq.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- COMPARISON_SUITABILITY: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- DOWNGRADE_REASON: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- OVERALL: Overall score capped because extracellular-vesicle samples are not ordinary tissue bulk RNA-seq.
- DOWNGRADE_REASON: Overall score capped because extracellular-vesicle samples are not ordinary tissue bulk RNA-seq.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is an extracellular-vesicle or exosome dataset.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- WARNING_CODE: EXTRACELLULAR_VESICLE_CONTEXT [warning]: Extracellular vesicle or exosome context was detected and may not represent ordinary tissue bulk RNA-seq.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 
- EXTRACELLULAR_VESICLE_CONTEXT [WARNING]: Extracellular vesicle or exosome context was detected and may not represent ordinary tissue bulk RNA-seq.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE301818

Dataset does not meet the current suitability threshold.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- DOWNGRADE_REASON: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
- DOWNGRADE_REASON: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 

### GSE301821

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Cell line. Comparison suitability: 0%.
- Downgraded for tissue search because it is a model-system experiment.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis vs healthy control.
- COMPARISON_SUITABILITY: Excluded sample type flags reduce suitability.
- DOWNGRADE_REASON: Excluded sample type flags reduce suitability.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Organoid or cell-line experiment downgraded for patient tissue search intent.
- DOWNGRADE_REASON: Organoid or cell-line experiment downgraded for patient tissue search intent.
- COMPARISON_SUITABILITY: Excluded model-system sample markers reduce suitability.
- DOWNGRADE_REASON: Excluded model-system sample markers reduce suitability.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a model-system experiment.
- WARNING_CODE: MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected.
- WARNING_CODE: CELL_LINES_INCLUDED [warning]: Cell line samples appear to be included.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- MIXED_SAMPLE_TYPES [WARNING]: Multiple sample type labels or exclusion flags were detected.; samples: 
- CELL_LINES_INCLUDED [WARNING]: Cell line samples appear to be included.; samples: GSM9090420, GSM9090422, GSM9090424, GSM9090425, GSM9090426, GSM9090427, GSM9090428, GSM9090429, GSM9090430, GSM9090431, GSM9090432, GSM9090433, GSM9090434, GSM9090435, GSM9090436, GSM9090437
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 

### GSE302306

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Infectious disease or host response, Sepsis, Septic shock.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs mixed controls.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 

### GSE32707

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis, Systemic inflammatory response syndrome.
- Processed data is available for downstream review.
- External evidence: PubMed links 21 publications; 21 DOIs available: PMID 22461369, PMID 36765335, PMID 37700323, PMID 38440848, PMID 38484574.
- Publication context: Inflammasome-regulated cytokines are critical mediators of acute lung injury.. American journal of respiratory and critical care medicine, 2012. PMID 22461369. DOI 10.1164/rccm.201201-0003OC.
- Publication context: Revealing novel pyroptosis-related therapeutic targets for sepsis based on machine learning.. BMC medical genomics, 2023. PMID 36765335. DOI 10.1186/s12920-023-01453-7.
- Publication context: A diagnostic model for sepsis-induced acute lung injury using a consensus machine learning approach and its therapeutic implications.. Journal of translational medicine, 2023. PMID 37700323. DOI 10.1186/s12967-023-04499-4.
- Publication context: 18 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs untreated.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE46955

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 7 publications; 7 DOIs available: PMID 25746953, PMID 31567880, PMID 33335583, PMID 33875577, PMID 39405478.
- Publication context: Human monocytes undergo functional re-programming during sepsis mediated by hypoxia-inducible factor-1α.. Immunity, 2015. PMID 25746953. DOI 10.1016/j.immuni.2015.02.001.
- Publication context: Screening key genes and microRNAs in sepsis by RNA-sequencing.. Journal of the Chinese Medical Association : JCMA, 2020. PMID 31567880. DOI 10.1097/JCMA.0000000000000209.
- Publication context: Identification of miR-4793-3p as a potential biomarker for bacterial infection in patients with hepatitis B virus-related liver cirrhosis: A pilot study.. Experimental and therapeutic medicine, 2021. PMID 33335583. DOI 10.3892/etm.2020.9552.
- Publication context: 4 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: 

### GSE48080

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis, Septic shock, Severe sepsis, Systemic inflammatory response syndrome.
- Processed data is available for downstream review.
- External evidence: PubMed links 6 publications; 6 DOIs available: PMID 24667684, PMID 26484123, PMID 32617294, PMID 37449204, PMID 38090272.
- Publication context: Patterns of gene expression in peripheral blood mononuclear cells and outcomes from patients with sepsis secondary to community acquired pneumonia.. PloS one, 2014. PMID 24667684. DOI 10.1371/journal.pone.0091886.
- Publication context: Gene expression profiling of mononuclear cells from patients with sepsis secondary to community-acquired pneumonia.. Genomics data, 2014. PMID 26484123. DOI 10.1016/j.gdata.2014.10.004.
- Publication context: The activation of IL-17 signaling pathway promotes pyroptosis in pneumonia-induced sepsis.. Annals of translational medicine, 2020. PMID 32617294. DOI 10.21037/atm-19-1739.
- Publication context: 3 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: 

### GSE54514

Dataset does not meet the current suitability threshold.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 21 publications; 21 DOIs available: PMID 23807251, PMID 37921181, PMID 38263335, PMID 38447501, PMID 38702721.
- Publication context: Identifying key regulatory genes in the whole blood of septic patients to monitor underlying immune dysfunctions.. Shock (Augusta, Ga.), 2013. PMID 23807251. DOI 10.1097/SHK.0b013e31829ee604.
- Publication context: Evidence from Machine Learning, Diagnostic Hub Genes in Sepsis and Diagnostic Models based on Xgboost Models, Novel Molecular Models for the Diagnosis of Sepsis.. Current medicinal chemistry, 2024. PMID 37921181. DOI 10.2174/0109298673273009231017061448.
- Publication context: Development of macrophage-associated genes prognostic signature predicts clinical outcome and immune infiltration for sepsis.. Scientific reports, 2024. PMID 38263335. DOI 10.1038/s41598-024-51536-3.
- Publication context: 18 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE63311

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis, Systemic inflammatory response syndrome.
- Processed data is available for downstream review.
- External evidence: recount3 reports trusted processed count availability.
- External evidence: PubMed links 2 publications; 2 DOIs available: PMID 25685830, PMID 41666610.
- Publication context: An Endotoxin Tolerance Signature Predicts Sepsis and Organ Dysfunction at Initial Clinical Presentation.. EBioMedicine, 2014. PMID 25685830. DOI 10.1016/j.ebiom.2014.10.003.
- Publication context: Unveiling the therapeutic potential of Resveratrol against neutrophil-mediated hyperinflammation in sepsis: An in-silico, molecular docking, and ex-vivo approach.. Biochemical and biophysical research communications, 2026. PMID 41666610. DOI 10.1016/j.bbrc.2026.153426.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE6535

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 5 publications; 4 DOIs available: PMID 18379237, PMID 23036193, PMID 28714002, PMID 31292051, PMID 35223539.
- Publication context: Gene-expression profiling of gram-positive and gram-negative sepsis in critically ill patients.. Critical care medicine, 2008. PMID 18379237. DOI 10.1097/CCM.0b013e3181692c0b.
- Publication context: Identification of sepsis subtypes in critically ill adults using gene expression profiling.. Critical care (London, England), 2012. PMID 23036193. DOI 10.1186/cc11667.
- Publication context: Identification of key genes in Gram‑positive and Gram‑negative sepsis using stochastic perturbation.. Molecular medicine reports, 2017. PMID 28714002. DOI 10.3892/mmr.2017.7013.
- Publication context: 2 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: 

### GSE65517

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Breast cancer, Sepsis, Tuberculosis.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 25992611.
- Publication context: Systemic Monocytic-MDSCs Are Generated from Monocytes and Correlate with Disease Progression in Breast Cancer Patients.. PloS one, 2015. PMID 25992611. DOI 10.1371/journal.pone.0127028.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: tumor sample vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: 

### GSE65682

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Metabolic disease, Sepsis, Septic shock.
- Processed data is available for downstream review.
- External evidence: PubMed links 36 publications; 36 DOIs available: PMID 26121490, PMID 26871709, PMID 26950237, PMID 26956172, PMID 27267747.
- Publication context: A molecular biomarker to diagnose community-acquired pneumonia on intensive care unit admission.. American journal of respiratory and critical care medicine, 2015. PMID 26121490. DOI 10.1164/rccm.201502-0355OC.
- Publication context: The Impact of HIV Co-Infection on the Genomic Response to Sepsis.. PloS one, 2016. PMID 26871709. DOI 10.1371/journal.pone.0148955.
- Publication context: Broad defects in the energy metabolism of leukocytes underlie immunoparalysis in sepsis.. Nature immunology, 2016. PMID 26950237. DOI 10.1038/ni.3398.
- Publication context: 33 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis vs normal tissue.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE66099

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis, Septic shock, Systemic inflammatory response syndrome.
- Processed data is available for downstream review.
- External evidence: PubMed links 11 publications; 11 DOIs available: PMID 25972003, PMID 27635771, PMID 30547887, PMID 33667236, PMID 37009294.
- Publication context: A comprehensive time-course-based multicohort analysis of sepsis and sterile inflammation reveals a robust diagnostic gene set.. Science translational medicine, 2015. PMID 25972003. DOI 10.1126/scitranslmed.aaa5993.
- Publication context: Olfactomedin-4 Is a Candidate Marker for a Pathogenic Neutrophil Subset in Septic Shock.. Critical care medicine, 2017. PMID 27635771. DOI 10.1097/CCM.0000000000002102.
- Publication context: Cytokine and molecular networks in sepsis cases: a network biology approach.. European cytokine network, 2018. PMID 30547887. DOI 10.1684/ecn.2018.0414.
- Publication context: 8 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: septicshock vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: THIRD_PARTY_REANALYSIS [warning]: This record is a third-party integration or reanalysis of public datasets. The GEO sample count may describe deposited atlas records rather than one independent clinical cohort; verify source-study provenance before analysis.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- THIRD_PARTY_REANALYSIS [WARNING]: This record is a third-party integration or reanalysis of public datasets. The GEO sample count may describe deposited atlas records rather than one independent clinical cohort; verify source-study provenance before analysis.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE72326

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Mixed specimen/source. Comparison suitability: 0%.
- Downgraded for tissue search because specimen/source classes are mixed.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Lupus erythematosus, Sepsis, Systemic lupus erythematosus.
- Processed data is available for downstream review.
- External evidence: PubMed links 8 publications; 8 DOIs available: PMID 36737814, PMID 37313407, PMID 37769649, PMID 38765814, PMID 39845969.
- Publication context: Incorporating knowledge of disease-defining hub genes and regulatory network into a machine learning-based model for predicting treatment response in lupus nephritis after the first renal flare.. Journal of translational medicine, 2023. PMID 36737814. DOI 10.1186/s12967-023-03931-z.
- Publication context: Cuproptosis-related gene identification and immune infiltration analysis in systemic lupus erythematosus.. Frontiers in immunology, 2023. PMID 37313407. DOI 10.3389/fimmu.2023.1157196.
- Publication context: Identification of monocyte-associated biomarkers in systemic lupus erythematosus and their pan-cancer analysis.. Lupus, 2023. PMID 37769649. DOI 10.1177/09612033231204765.
- Publication context: 5 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: systemic lupus erythematosus vs mixed controls.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Mixed specimen/source dataset downgraded until tissue samples are clearly separated.
- DOWNGRADE_REASON: Mixed specimen/source dataset downgraded until tissue samples are clearly separated.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because specimen/source classes are mixed.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: 

### GSE8121

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis, Septic shock.
- Processed data is available for downstream review.
- External evidence: PubMed links 4 publications; 4 DOIs available: PMID 17932561, PMID 39315170, PMID 39636505, PMID 40597679.
- Publication context: Genome-level longitudinal expression of signaling pathways and gene networks in pediatric septic shock.. Molecular medicine (Cambridge, Mass.), 2007. PMID 17932561. DOI 10.2119/2007-00065.Shanley.
- Publication context: Data-driven analysis that integrates bioinformatics and machine learning uncovers PANoptosis-related diagnostic genes in early pediatric septic shock.. Heliyon, 2024. PMID 39315170. DOI 10.1016/j.heliyon.2024.e37853.
- Publication context: Identification of common core genes and pathways in childhood sepsis and cancer by bioinformatics analysis.. Discover oncology, 2024. PMID 39636505. DOI 10.1007/s12672-024-01651-4.
- Publication context: 1 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE9692

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis, Septic shock.
- Processed data is available for downstream review.
- External evidence: Expression Atlas curated experiment link is available.
- External evidence: PubMed links 6 publications; 5 DOIs available: PMID 18460642, PMID 35190763, PMID 37089399, PMID 37235492, PMID 37359526.
- Publication context: Validating the genomic signature of pediatric septic shock.. Physiological genomics, 2008. PMID 18460642. DOI 10.1152/physiolgenomics.00025.2008.
- Publication context: Analysis of Sepsis Markers and Pathogenesis Based on Gene Differential Expression and Protein Interaction Network.. Journal of healthcare engineering, 2022. PMID 35190763. DOI 10.1155/2022/6878495.
- Publication context: Identification of potential biomarkers and pathways for sepsis using RNA sequencing technology and bioinformatic analysis.. Heliyon, 2023. PMID 37089399. DOI 10.1016/j.heliyon.2023.e15034.
- Publication context: 3 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs normal tissue.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE9960

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis, Systemic inflammatory response syndrome.
- Processed data is available for downstream review.
- External evidence: PubMed links 14 publications; 14 DOIs available: PMID 19237892, PMID 19535937, PMID 30547887, PMID 33448176, PMID 33737824.
- Publication context: Gene-expression profiling of peripheral blood mononuclear cells in sepsis.. Critical care medicine, 2009. PMID 19237892. DOI 10.1097/CCM.0b013e31819b52fd.
- Publication context: Gene-expression profiling of peripheral blood mononuclear cells in sepsis.. Critical care medicine, 2009. PMID 19535937. DOI 10.1097/CCM.0b013e3181aab5a3.
- Publication context: Cytokine and molecular networks in sepsis cases: a network biology approach.. European cytokine network, 2018. PMID 30547887. DOI 10.1684/ecn.2018.0414.
- Publication context: 11 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: 

### GSE104423

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: recount3 reports trusted processed count availability.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 29236770.
- Publication context: Association between preoperative peripheral blood mononuclear cell gene expression profiles, early postoperative organ function recovery potential and long-term survival in advanced heart failure patients undergoing mechanical circulatory support.. PloS one, 2017. PMID 29236770. DOI 10.1371/journal.pone.0189420.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE10474

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 13 publications; 12 DOIs available: PMID 19174476, PMID 23661517, PMID 25257390, PMID 29805488, PMID 31623626.
- Publication context: Discovery of the gene signature for acute lung injury in patients with sepsis.. Physiological genomics, 2009. PMID 19174476. DOI 10.1152/physiolgenomics.90275.2008.
- Publication context: DNA microarray-based screening of differentially expressed genes related to acute lung injury and functional analysis.. European review for medical and pharmacological sciences, 2013. PMID 23661517.
- Publication context: Gene expression profiles analysis identifies key genes for acute lung injury in patients with sepsis.. Diagnostic pathology, 2014. PMID 25257390. DOI 10.1186/s13000-014-0176-x.
- Publication context: 10 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE110487

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Sepsis, Septic shock.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE119217

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis, Severe sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 3 publications; 3 DOIs available: PMID 31983492, PMID 35082520, PMID 35198634.
- Publication context: Gene Expression Profiles in Children With Suspected Sepsis.. Annals of emergency medicine, 2020. PMID 31983492. DOI 10.1016/j.annemergmed.2019.09.020.
- Publication context: CD63 and C3AR1: The Potential Molecular Targets in the Progression of Septic Shock.. International journal of general medicine, 2022. PMID 35082520. DOI 10.2147/IJGM.S338486.
- Publication context: Identification of a Four-Gene Signature for Diagnosing Paediatric Sepsis.. BioMed research international, 2022. PMID 35198634. DOI 10.1155/2022/5217885.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE121350

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Septic shock.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE123729

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis, Septic shock, Systemic inflammatory response syndrome.
- Processed data is available for downstream review.
- External evidence: PubMed links 2 publications; 2 DOIs available: PMID 31075840, PMID 35844509.
- Publication context: AKIRIN1: A Potential New Reference Gene in Human Natural Killer Cells and Granulocytes in Sepsis.. International journal of molecular sciences, 2019. PMID 31075840. DOI 10.3390/ijms20092290.
- Publication context: Key Signature Genes of Early Terminal Granulocytic Differentiation Distinguish Sepsis From Systemic Inflammatory Response Syndrome on Intensive Care Unit Admission.. Frontiers in immunology, 2022. PMID 35844509. DOI 10.3389/fimmu.2022.864835.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 
- INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: 

### GSE123730

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis, Septic shock, Systemic inflammatory response syndrome.
- Processed data is available for downstream review.
- External evidence: PubMed links 2 publications; 2 DOIs available: PMID 31075840, PMID 35844509.
- Publication context: AKIRIN1: A Potential New Reference Gene in Human Natural Killer Cells and Granulocytes in Sepsis.. International journal of molecular sciences, 2019. PMID 31075840. DOI 10.3390/ijms20092290.
- Publication context: Key Signature Genes of Early Terminal Granulocytic Differentiation Distinguish Sepsis From Systemic Inflammatory Response Syndrome on Intensive Care Unit Admission.. Frontiers in immunology, 2022. PMID 35844509. DOI 10.3389/fimmu.2022.864835.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 
- INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: 

### GSE12624

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis, Septic shock, Severe sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 6 publications; 5 DOIs available: PMID 24668717, PMID 28565754, PMID 29642183, PMID 31059023, PMID 37449204.
- Publication context: Screening of differentially expressed genes related to severe sepsis induced by multiple trauma with DNA microarray.. European review for medical and pharmacological sciences, 2014. PMID 24668717.
- Publication context: Identification of potential biomarkers of sepsis using bioinformatics analysis.. Experimental and therapeutic medicine, 2017. PMID 28565754. DOI 10.3892/etm.2017.4178.
- Publication context: Identification of genes related to consecutive trauma-induced sepsis via gene expression profiling analysis.. Medicine, 2018. PMID 29642183. DOI 10.1097/MD.0000000000010362.
- Publication context: 3 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE133822

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE135838

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%.
- Downgraded for tissue search because study design or specimen source is unclear.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE138712

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 2 publications; 2 DOIs available: PMID 32479514, PMID 37113992.
- Publication context: Whole blood transcriptional responses of very preterm infants during late-onset sepsis.. PloS one, 2020. PMID 32479514. DOI 10.1371/journal.pone.0233841.
- Publication context: Gene filtering strategies for machine learning guided biomarker discovery using neonatal sepsis RNA-seq data.. Frontiers in genetics, 2023. PMID 37113992. DOI 10.3389/fgene.2023.1158352.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE150707

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis, Severe sepsis, Systemic inflammatory response syndrome.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE157737

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Breast cancer, Melanoma, Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 32958605.
- Publication context: Human G-MDSCs are neutrophils at distinct maturation stages promoting tumor growth in breast cancer.. Life science alliance, 2020. PMID 32958605. DOI 10.26508/lsa.202000893.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE168440

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis, Systemic inflammatory response syndrome.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE168442

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis, Systemic inflammatory response syndrome.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE180387

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Sepsis, Septic shock.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE182522

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 34977060.
- Publication context: Using RNA-Seq to Investigate Immune-Metabolism Features in Immunocompromised Patients With Sepsis.. Frontiers in medicine, 2021. PMID 34977060. DOI 10.3389/fmed.2021.747263.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE198103

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Colorectal cancer, Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 36450776.
- Publication context: Transcriptome profiling of colorectal tumors from patients with sepsis reveals an ethnic basis for viral infection risk and sepsis progression.. Scientific reports, 2022. PMID 36450776. DOI 10.1038/s41598-022-24489-8.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE20568

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 20477762.
- Publication context: Genes associated with alcohol abuse and tobacco smoking in the human nucleus accumbens and ventral tegmental area.. Alcoholism, clinical and experimental research, 2010. PMID 20477762. DOI 10.1111/j.1530-0277.2010.01207.x.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE208581

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Infectious disease or host response, Sepsis, Systemic inflammatory response syndrome.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE208587

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: COVID-19, Infectious disease or host response, Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE211210

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE233322

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE239388

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%.
- Downgraded for tissue search because study design or specimen source is unclear.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 2 publications; 2 DOIs available: PMID 37638006, PMID 40544732.
- Publication context: Activation of thousands of genes in the lungs and kidneys by sepsis is countered by the selective nuclear blockade.. Frontiers in immunology, 2023. PMID 37638006. DOI 10.3389/fimmu.2023.1221102.
- Publication context: Tanshinone IIA attenuates sepsis-induced lung injury by reducing VEGFR2/PI3K/AKT-driven mitochondrial disruption dependent apoptosis.. Phytomedicine : international journal of phytotherapy and phytopharmacology, 2025. PMID 40544732. DOI 10.1016/j.phymed.2025.156957.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because non-human datasets are outside the selected human ranking intent.
- DOWNGRADE_REASON: Overall score capped because non-human datasets are outside the selected human ranking intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [critical]: Dataset organism does not match the human patient-tissue tumor-normal intent.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- INTENT_ASSAY_MISMATCH [CRITICAL]: Dataset organism does not match the human patient-tissue tumor-normal intent.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE264050

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Cell line. Comparison suitability: 0%.
- Downgraded for tissue search because it is a model-system experiment.
- Downgraded for tissue search because study design or specimen source is unclear.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Fibrosis, Idiopathic pulmonary fibrosis, Infectious disease or host response, Lung fibrosis, Metabolic disease, Parkinson disease, Prostate cancer, Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: Excluded sample type flags reduce suitability.
- DOWNGRADE_REASON: Excluded sample type flags reduce suitability.
- COMPARISON_SUITABILITY: Organoid or cell-line experiment downgraded for patient tissue search intent.
- DOWNGRADE_REASON: Organoid or cell-line experiment downgraded for patient tissue search intent.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Excluded model-system sample markers reduce suitability.
- DOWNGRADE_REASON: Excluded model-system sample markers reduce suitability.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Cell line. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a model-system experiment.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected.
- WARNING_CODE: CELL_LINES_INCLUDED [warning]: Cell line samples appear to be included.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MIXED_SAMPLE_TYPES [WARNING]: Multiple sample type labels or exclusion flags were detected.; samples: 
- CELL_LINES_INCLUDED [WARNING]: Cell line samples appear to be included.; samples: GSM8209246, GSM8209247, GSM8209248, GSM8209249, GSM8209250, GSM8209251, GSM8209252, GSM8209253, GSM8209254, GSM8209255, GSM8209256, GSM8209257, GSM8209258, GSM8209259, GSM8209260, GSM8209261, GSM8209262, GSM8209263, GSM8209264, GSM8209265, GSM8209266, GSM8209267, GSM8209268, GSM8209269, GSM8209270, GSM8209271, GSM8209272, GSM8209273, GSM8209274, GSM8209275, GSM8209276, GSM8209277, GSM8209278, GSM8209279, GSM8209280, GSM8209281, GSM8209282, GSM8209283, GSM8209284, GSM8209285, GSM8209286, GSM8209287, GSM8209288, GSM8209289, GSM8209290, GSM8209291, GSM8209292, GSM8209293, GSM8209294, GSM8209295, GSM8209296, GSM8209297, GSM8209298, GSM8209299, GSM8209300, GSM8209301, GSM8209302, GSM8209303, GSM8209304, GSM8209305, GSM8209306, GSM8209307, GSM8209308, GSM8209309, GSM8209310, GSM8209311, GSM8209312, GSM8209313, GSM8209314, GSM8209315, GSM8209316, GSM8209317, GSM8209318, GSM8209319, GSM8209320, GSM8209321, GSM8209322, GSM8209323, GSM8209324, GSM8209325, GSM8209326, GSM8209327, GSM8209328, GSM8209329, GSM8209330, GSM8209331, GSM8209332
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE282464

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: COVID-19, Infectious disease or host response, Sepsis, Septic shock.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 40640204.
- Publication context: Molecular landscape of respiratory infection: A large-scale, multi-centre blood transcriptome dataset.. Scientific data, 2025. PMID 40640204. DOI 10.1038/s41597-025-05488-6.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE296830

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Infectious disease or host response, Sepsis, Septic shock, Severe sepsis, Systemic inflammatory response syndrome.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 41690949.
- Publication context: A dataset of paired blood mRNA and microRNA sequencing across acute septic shock and recovery.. Scientific data, 2026. PMID 41690949. DOI 10.1038/s41597-026-06844-w.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- DOWNGRADE_REASON: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
- DOWNGRADE_REASON: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE316708

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Infectious disease or host response, Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE4607

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis, Septic shock, Severe sepsis, Systemic inflammatory response syndrome.
- Processed data is available for downstream review.
- External evidence: PubMed links 13 publications; 13 DOIs available: PMID 17374846, PMID 18460642, PMID 18511707, PMID 23107287, PMID 32016447.
- Publication context: Genome-level expression profiles in pediatric septic shock indicate a role for altered zinc homeostasis in poor outcome.. Physiological genomics, 2007. PMID 17374846. DOI 10.1152/physiolgenomics.00024.2007.
- Publication context: Validating the genomic signature of pediatric septic shock.. Physiological genomics, 2008. PMID 18460642. DOI 10.1152/physiolgenomics.00025.2008.
- Publication context: Interleukin-8 as a stratification tool for interventional trials involving pediatric septic shock.. American journal of respiratory and critical care medicine, 2008. PMID 18511707. DOI 10.1164/rccm.200801-131OC.
- Publication context: 10 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE5262

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis, Septic shock.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE5271

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE63042

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Infectious disease or host response, Sepsis, Septic shock, Severe sepsis, Systemic inflammatory response syndrome.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE64498

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Melanoma, Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 26817997.
- Publication context: Post-Sepsis State Induces Tumor-Associated Macrophage Accumulation through CXCR4/CXCL12 and Favors Tumor Progression in Mice.. Cancer immunology research, 2016. PMID 26817997. DOI 10.1158/2326-6066.CIR-15-0170.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because non-human datasets are outside the selected human ranking intent.
- DOWNGRADE_REASON: Overall score capped because non-human datasets are outside the selected human ranking intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [critical]: Dataset organism does not match the human patient-tissue tumor-normal intent.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [CRITICAL]: Dataset organism does not match the human patient-tissue tumor-normal intent.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE66890

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 16 publications; 16 DOIs available: PMID 25795726, PMID 31623626, PMID 34393665, PMID 35538832, PMID 36552336.
- Publication context: Increased expression of neutrophil-related genes in patients with early sepsis-induced ARDS.. American journal of physiology. Lung cellular and molecular physiology, 2015. PMID 25795726. DOI 10.1152/ajplung.00380.2014.
- Publication context: DNA methylation exploration for ARDS: a multi-omics and multi-microarray interrelated analysis.. Journal of translational medicine, 2019. PMID 31623626. DOI 10.1186/s12967-019-2090-1.
- Publication context: A Five-Genes Based Diagnostic Signature for Sepsis-Induced ARDS.. Pathology oncology research : POR, 2021. PMID 34393665. DOI 10.3389/pore.2021.580801.
- Publication context: 13 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE69528

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Metabolic disease, Sepsis, Type 2 diabetes.
- Processed data is available for downstream review.
- External evidence: PubMed links 14 publications; 13 DOIs available: PMID 19903332, PMID 34760021, PMID 36199375, PMID 36518055, PMID 38227599.
- Publication context: Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis.. Genome biology, 2009. PMID 19903332. DOI 10.1186/gb-2009-10-11-r127.
- Publication context: Bioinformatics Analysis for Identifying Pertinent Pathways and Genes in Sepsis.. Computational and mathematical methods in medicine, 2021. PMID 34760021. DOI 10.1155/2021/2085173.
- Publication context: Screening of Sepsis Biomarkers Based on Bioinformatics Data Analysis.. Journal of healthcare engineering, 2022. PMID 36199375. DOI 10.1155/2022/6788569.
- Publication context: 11 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE69686

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 7 publications; 7 DOIs available: PMID 26052715, PMID 27114524, PMID 36855207, PMID 40177399, PMID 41113854.
- Publication context: Postnatal Age Is a Critical Determinant of the Neonatal Host Response to Sepsis.. Molecular medicine (Cambridge, Mass.), 2015. PMID 26052715. DOI 10.2119/molmed.2015.00064.
- Publication context: Targeting IL-17A attenuates neonatal sepsis mortality induced by IL-18.. Proceedings of the National Academy of Sciences of the United States of America, 2016. PMID 27114524. DOI 10.1073/pnas.1515793113.
- Publication context: Identification and verification of feature biomarkers associated with immune cells in neonatal sepsis.. European journal of medical research, 2023. PMID 36855207. DOI 10.1186/s40001-023-01061-2.
- Publication context: 4 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE70311

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 26727089.
- Publication context: An Integrated Clinico-transcriptomic Approach Identifies a Central Role of the Heme Degradation Pathway for Septic Complications after Trauma.. Annals of surgery, 2016. PMID 26727089. DOI 10.1097/SLA.0000000000001553.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 
- INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: 

### GSE70461

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 28259955.
- Publication context: Gene expression profiles in preterm infants on continuous long‑term oxygen therapy suggest reduced oxidative stress‑dependent signaling during hypoxia.. Molecular medicine reports, 2017. PMID 28259955. DOI 10.3892/mmr.2017.6185.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- DOWNGRADE_REASON: Publication context: Gene expression profiles in preterm infants on continuous long‑term oxygen therapy suggest reduced oxidative stress‑dependent signaling during hypoxia.. Molecular medicine reports, 2017. PMID 28259955. DOI 10.3892/mmr.2017.6185.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM1755272
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE74224

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis, Systemic inflammatory response syndrome.
- Processed data is available for downstream review.
- External evidence: PubMed links 3 publications; 3 DOIs available: PMID 26645559, PMID 36552336, PMID 38912048.
- Publication context: A Molecular Host Response Assay to Discriminate Between Sepsis and Infection-Negative Systemic Inflammation in Critically Ill Patients: Discovery and Validation in Independent Cohorts.. PLoS medicine, 2015. PMID 26645559. DOI 10.1371/journal.pmed.1001916.
- Publication context: Drug Repurposing Using Gene Co-Expression and Module Preservation Analysis in Acute Respiratory Distress Syndrome (ARDS), Systemic Inflammatory Response Syndrome (SIRS), Sepsis, and COVID-19.. Biology, 2022. PMID 36552336. DOI 10.3390/biology11121827.
- Publication context: Identification of key genes as potential diagnostic biomarkers in sepsis by bioinformatics analysis.. PeerJ, 2024. PMID 38912048. DOI 10.7717/peerj.17542.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE84439

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: recount3 reports trusted processed count availability.
- External evidence: PubMed links 3 publications; 3 DOIs available: PMID 30665420, PMID 37565892, PMID 39495350.
- Publication context: Whole blood RNA sequencing reveals a unique transcriptomic profile in patients with ARDS following hematopoietic stem cell transplantation.. Respiratory research, 2019. PMID 30665420. DOI 10.1186/s12931-019-0981-6.
- Publication context: Genome-wide analysis of RNA-binding protein co-expression with alternative splicing events in acute respiratory distress syndrome following hematopoietic stem cell transplantation.. Medicine, 2023. PMID 37565892. DOI 10.1097/MD.0000000000034599.
- Publication context: Clinical significance and potential mechanism of hsa_circ_0006892 in acute respiratory distress syndrome complicated with pulmonary fibrosis.. Molecular biology reports, 2024. PMID 39495350. DOI 10.1007/s11033-024-10047-0.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE94717

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- DOWNGRADE_REASON: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
- DOWNGRADE_REASON: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE101639

Dataset does not meet the current suitability threshold.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis, Septic shock.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- COMPARISON_SUITABILITY: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- DOWNGRADE_REASON: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized.
- MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because fewer than ten samples limit cohort confidence.
- DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE13205

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 10 publications; 9 DOIs available: PMID 18997871, PMID 24254554, PMID 29512785, PMID 30914088, PMID 32008037.
- Publication context: Dysregulation of mitochondrial dynamics and the muscle transcriptome in ICU patients suffering from sepsis induced multiple organ failure.. PloS one, 2008. PMID 18997871. DOI 10.1371/journal.pone.0003686.
- Publication context: Comparative gene expression profiling reveals key pathways in septic skeletal muscle.. European review for medical and pharmacological sciences, 2013. PMID 24254554.
- Publication context: Identification of potential genes and miRNAs associated with sepsis based on microarray analysis.. Molecular medicine reports, 2018. PMID 29512785. DOI 10.3892/mmr.2018.8668.
- Publication context: 7 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- COMPARISON_SUITABILITY: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- DOWNGRADE_REASON: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized.
- MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- TISSUE_TYPE_MISSING [WARNING]: Tissue or cell type could not be normalized.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: 

### GSE149764

Dataset does not meet the current suitability threshold.

- Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- DOWNGRADE_REASON: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized.
- MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
- DOWNGRADE_REASON: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 

### GSE184803

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Extracellular vesicle. Comparison suitability: 0%.
- Downgraded for tissue search because it is an extracellular-vesicle or exosome dataset.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 35187084.
- Publication context: Diagnostic Potential of Plasma Extracellular Vesicle miR-483-3p and Let-7d-3p for Sepsis.. Frontiers in molecular biosciences, 2022. PMID 35187084. DOI 10.3389/fmolb.2022.814240.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Extracellular-vesicle or exosome dataset downgraded because this ranking targets ordinary tissue bulk RNA-seq.
- DOWNGRADE_REASON: Extracellular-vesicle or exosome dataset downgraded because this ranking targets ordinary tissue bulk RNA-seq.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- COMPARISON_SUITABILITY: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- DOWNGRADE_REASON: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized.
- MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because fewer than ten samples limit cohort confidence.
- DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- OVERALL: Overall score capped because extracellular-vesicle samples are not ordinary tissue bulk RNA-seq.
- DOWNGRADE_REASON: Overall score capped because extracellular-vesicle samples are not ordinary tissue bulk RNA-seq.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is an extracellular-vesicle or exosome dataset.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- WARNING_CODE: EXTRACELLULAR_VESICLE_CONTEXT [warning]: Extracellular vesicle or exosome context was detected and may not represent ordinary tissue bulk RNA-seq.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 
- EXTRACELLULAR_VESICLE_CONTEXT [WARNING]: Extracellular vesicle or exosome context was detected and may not represent ordinary tissue bulk RNA-seq.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE210797

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Infectious disease or host response, Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Control type metadata detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized.
- MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.

### GSE252275

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Sepsis, Severe sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized.
- MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 

### GSE294059

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized.
- MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 

### GSE310375

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 41792260.
- Publication context: β-Nicotinamide mononucleotide preserves muscle strength in septic male mice.. Scientific reports, 2026. PMID 41792260. DOI 10.1038/s41598-026-43172-w.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized.
- MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because non-human datasets are outside the selected human ranking intent.
- DOWNGRADE_REASON: Overall score capped because non-human datasets are outside the selected human ranking intent.
- OVERALL: Overall score capped because fewer than ten samples limit cohort confidence.
- DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [critical]: Dataset organism does not match the human patient-tissue tumor-normal intent.
- INTENT_ASSAY_MISMATCH [CRITICAL]: Dataset organism does not match the human patient-tissue tumor-normal intent.; samples: 

### GSE5772

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 2 publications; 2 DOIs available: PMID 17575094, PMID 23036193.
- Publication context: The use of gene-expression profiling to identify candidate genes in human sepsis.. American journal of respiratory and critical care medicine, 2007. PMID 17575094. DOI 10.1164/rccm.200612-1819OC.
- Publication context: Identification of sepsis subtypes in critically ill adults using gene expression profiling.. Critical care (London, England), 2012. PMID 23036193. DOI 10.1186/cc11667.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized.
- MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- TISSUE_TYPE_MISSING [WARNING]: Tissue or cell type could not be normalized.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: 

### GSE89376

Dataset does not meet the current suitability threshold.

- Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 3 publications; 3 DOIs available: PMID 34053485, PMID 35774747, PMID 41198548.
- Publication context: [Construction of sepsis-associated competing endogenous RNA network based on Gene Expression Omnibus datasets and bioinformatic analysis].. Zhonghua wei zhong bing ji jiu yi xue, 2021. PMID 34053485. DOI 10.3760/cma.j.cn121430-20210205-00211.
- Publication context: Characterization of lncRNA-Based ceRNA Network and Potential Prognostic Hub Genes for Sepsis.. Evidence-based complementary and alternative medicine : eCAM, 2022. PMID 35774747. DOI 10.1155/2022/1485033.
- Publication context: Calcitonin Alleviates Sepsis-Induced Acute Lung Injury by Inhibiting the HMGB1/MyD88/NF-κB Pathway by Targeting CD3D.. Frontiers in bioscience (Landmark edition), 2025. PMID 41198548. DOI 10.31083/FBL44677.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- COMPARISON_SUITABILITY: Case and control sample groups detected: sepsis or systemic inflammatory response vs healthy control.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
- COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized.
- MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- TISSUE_TYPE_MISSING [WARNING]: Tissue or cell type could not be normalized.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: 

### GSE137341

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis, Septic shock, Severe sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- RELEVANCE: Anatomical source metadata normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- COMPARISON_SUITABILITY: Pooled or technical replicate samples reduce suitability.
- DOWNGRADE_REASON: Pooled or technical replicate samples reduce suitability.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: Pooled samples or technical replicates need review before trusting group counts.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: TECHNICAL_REPLICATES_DETECTED [warning]: Technical replicate samples were detected.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- TECHNICAL_REPLICATES_DETECTED [WARNING]: Technical replicate samples were detected.; samples: GSM4075825, GSM4075826
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE139913

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- Downgraded for tissue search because study design or specimen source is unclear.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized.
- MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- TISSUE_TYPE_MISSING [WARNING]: Tissue or cell type could not be normalized.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 
- INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: 

### GSE218494

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 2 publications; 2 DOIs available: PMID 36923408, PMID 40258759.
- Publication context: CircRNA_0075723 protects against pneumonia-induced sepsis through inhibiting macrophage pyroptosis by sponging miR-155-5p and regulating SHIP1 expression.. Frontiers in immunology, 2023. PMID 36923408. DOI 10.3389/fimmu.2023.1095457.
- Publication context: The critical immunoregulatory roles and molecular mechanisms of IL-10 and IL-18 genes in pneumonia and sepsis.. Medicine, 2025. PMID 40258759. DOI 10.1097/MD.0000000000042104.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized.
- MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized.
- METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because fewer than ten samples limit cohort confidence.
- DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE267399

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- Downgraded for tissue search because study design or specimen source is unclear.
- Prioritized assay: bulk RNA-seq is the active assay expectation.
- Interpreted disease metadata: Infectious disease or host response, Sepsis.
- Processed data is available for downstream review.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized.
- MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized.
- METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because fewer than ten samples limit cohort confidence.
- DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- TISSUE_TYPE_MISSING [WARNING]: Tissue or cell type could not be normalized.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 
- INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: 

### GSE79962

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 21 publications; 21 DOIs available: PMID 28067713, PMID 37559624, PMID 37759133, PMID 37872948, PMID 37974098.
- Publication context: Widespread Down-Regulation of Cardiac Mitochondrial and Sarcomeric Genes in Patients With Sepsis.. Critical care medicine, 2017. PMID 28067713. DOI 10.1097/CCM.0000000000002207.
- Publication context: Analysis of the role of glucose metabolism-related genes in dilated cardiomyopathy based on bioinformatics.. Journal of thoracic disease, 2023. PMID 37559624. DOI 10.21037/jtd-23-906.
- Publication context: DLK1 overexpression improves sepsis-induced cardiac dysfunction and fibrosis in mice through the TGF-β1/Smad3 signaling pathway and MMPs.. Journal of molecular histology, 2023. PMID 37759133. DOI 10.1007/s10735-023-10161-6.
- Publication context: 18 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized.
- MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE82315

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- Downgraded for tissue search because it is a biofluid cohort.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Infectious disease or host response, Sepsis.
- Processed data is available for downstream review.
- External evidence: PubMed links 1 publication; 1 DOI available: PMID 29078758.
- Publication context: Transcriptomic data from two primary cell models stimulating human monocytes suggest inhibition of oxidative phosphorylation and mitochondrial function by N. meningitidis which is partially up-regulated by IL-10.. BMC immunology, 2017. PMID 29078758. DOI 10.1186/s12865-017-0229-5.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized.
- MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized.
- METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM2188927, GSM2188928, GSM2188929, GSM2188930, GSM2188931, GSM2188932, GSM2188933, GSM2188934, GSM2188935, GSM2188936, GSM2188937, GSM2188938
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 

### GSE67652

Dataset does not meet the current suitability threshold.

- Comparison: Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- Downgraded for tissue search because study design or specimen source is unclear.
- Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- Interpreted disease metadata: Sepsis, Septic shock.
- Processed data is available for downstream review.
- External evidence: PubMed links 4 publications; 4 DOIs available: PMID 26047321, PMID 38702721, PMID 38755528, PMID 41198548.
- Publication context: Septic Shock in Advanced Age: Transcriptome Analysis Reveals Altered Molecular Signatures in Neutrophil Granulocytes.. PloS one, 2015. PMID 26047321. DOI 10.1371/journal.pone.0128341.
- Publication context: Identification of sepsis-associated mitochondrial genes through RNA and single-cell sequencing approaches.. BMC medical genomics, 2024. PMID 38702721. DOI 10.1186/s12920-024-01891-x.
- Publication context: Identification of four mitochondria-related genes in sepsis based on RNA sequencing technology.. BMC immunology, 2024. PMID 38755528. DOI 10.1186/s12865-024-00623-1.
- Publication context: 1 additional linked PubMed publications are available.
- RELEVANCE: Disease or condition metadata normalized.
- RELEVANCE: Organism normalized.
- RELEVANCE: Assay type normalized.
- COMPARISON_SUITABILITY: No excluded sample type flags detected.
- COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
- COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
- METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
- METADATA_QUALITY: Group clarity: Case and control groups are not clear from sample metadata.
- MISSING_METADATA: Missing or unclear metadata. Group clarity - Case and control groups are not clear from sample metadata.
- METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized.
- METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized.
- MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized.
- METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata.
- METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected.
- METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit.
- DATA_AVAILABILITY: Processed data available.
- DATA_AVAILABILITY: Raw data available.
- OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability.
- OVERALL: Overall score capped because comparison suitability is weak for the selected search intent.
- DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent.
- RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold.
- MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%.
- DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear.
- MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
- DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
- WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.
- WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.
- WARNING_CODE: TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized.
- WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
- WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
- WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.
- NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: 
- MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: 
- TISSUE_TYPE_MISSING [WARNING]: Tissue or cell type could not be normalized.; samples: 
- INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: 
- INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: 
- INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: