GSE230539

IPA analysis of CD14-positive monocytes/macrophages from IBD patients and controls

Whole-study status Not suitable

Dataset does not meet the current suitability threshold.

Whole-study downloads — these do not apply your sample requirements.

Selected cohort requirements

Samples meeting selected requirements: 0 cases / 0 controls

View matching samples

4 case / 4 control samples elsewhere in the study have incomplete or conflicting evidence; they are not included above

Patient pairs verified in indexed sample metadata: 0

A case/control comparison meeting these requirements is not confirmed.

Counts describe samples, not independent patients. Pair verification uses explicit subject identifiers in indexed sample metadata. Zero verified pairs does not establish that the study is unpaired; reported matched-normal design alone is insufficient.

Source: GEO
Assay: microarray
Organism: Homo sapiens
Whole-study samples: 8 samples
Specimen: Unclear specimen/source
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Weber S, Sonnewald S, Reid S, Simone W
Contact name: Weber Simone
Submission date: 2023-04-25
Last update: 2026-05-01
Organization: Friedrich-Alexander University Erlangen-Nuremberg
Department: Medicine
Public date: 2026-05-01
Experiment types: Expression profiling by array
Platforms: GPL13497 Agilent-026652 Whole Human Genome Microarray 4x44K v2 (Probe Name version)
Series type: Series
SubSeries: Not available
BioProject: PRJNA961719

Summary

the gene expression profiles of CD14-positive cells from IBD and control patients were analyzed

Overall design

CD14-positve cells were isolated from tissue samples from four IBD and four control patients

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 8 GSM samples	Primary source
recount3	Planned trusted source for processed count availability.	No match found
Expression Atlas	Planned source for curated expression experiment links.	No match found
PubMed	Publication context when PubMed identifiers are already known.	No match found

Metadata Quality Components

Persisted metadata quality

85 pts

Clarity: 85%
Weight: 100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata normalized. Tissue clarity: Tissue metadata was not normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.

Analysis Readiness

Ready after review

97% DE readiness

Contrast completeness

25/25 pts

Both case and control groups are present in the proposed grouping.

Minimum group size

20/20 pts

Each contrast group has at least 2 samples.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

15/15 pts

All samples are assigned to a case or control group.

Blocking warnings

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

No readiness blockers detected.

Next Steps

Verify the proposed sample assignments and case-versus-control comparison against the GEO metadata before using them in DESeq2 or another differential-expression tool.
Confirm processed count files and sample identifiers match the exported metadata.

Analysis Preparation Checklist

5/6 ready

Group labels reviewed

Needs review

Siftome proposed case and control labels, but no reviewer confirmation is stored yet.

Open the sample grouping CSV and confirm group labels before analysis.

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

Confirm whether the cohort is large enough for the intended statistical analysis.

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

Verify that downloaded processed files contain usable count or expression identifiers.

Ambiguous samples handled

Ready

No review-needed or unassigned samples are present in the proposed grouping.

Review the grouping table for biologically meaningful differences that the automated checks may not detect.

Exclusion decisions recorded

Ready

No hard-excluded samples were detected by the current rules.

Record any manual exclusions in the downstream analysis notes.

Source traceability preserved

Ready

The dataset and sample accessions can be traced back to GEO.

Keep GEO accessions with exported metadata.

Bioinformatician Review

Bioinformatician review required

Ask a bioinformatician to review grouping, count availability, exclusions, and design before DE.

Assay context may require expert handling before DESeq2-style analysis.

Why This Is Ranked Here

Tumor vs normal

Not suitable Dataset does not meet the current suitability threshold.

Applied Review Decisions

No active review decisions affect this ranking.

Derived Classifications

Assay differs from search intent Microarray Search intent expects bulk RNA-seq. Assay came from Normalization rules.
Disease context Inflammatory bowel disease Disease context came from Normalization rules.
Likely case group Inflammatory bowel disease 4 samples
Likely control group Control 4 samples

Intent Interpretation

Downgrade or exclusion reason Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

Interpreted disease metadata: Inflammatory bowel disease.
Processed data is available for downstream review.

Cautions

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.
Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized.
Overall score capped because comparison suitability is weak for the selected search intent.
Overall score capped because fewer than ten samples limit cohort confidence.
Missing or unclear metadata. Comparison - Disease/model vs control. Specimen - Unclear specimen/source. Comparison suitability: 0%.
Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Microarray expression context was detected; compare separately from RNA-seq cohorts.
Tissue or cell type could not be normalized.
Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.

Normalized Fields

7 fields

Field Value Source Derived by Confidence Evidence Reason

assay_type microarray GSE230539 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE230539 dataset_title: IPA analysis of CD14-positive monocytes/macrophages from IBD patients and controls organism: Homo sapiens assay_type: microarray proc... keyword match keyword match: microarray

disease inflammatory bowel disease GSE230539 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd dataset_accession: GSE230539 dataset_title: IPA analysis of CD14-positive monocytes/macrophages from IBD patients and controls organism: Homo sapiens assay_type: microarray proc... controlled vocabulary controlled vocabulary disease match: ibd

disease inflammatory bowel disease GSM7226501 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd IBD patient 1 Laminar propria mononuclear cell cell type: Laminar propria mononuclear cell controlled vocabulary controlled vocabulary disease match: ibd

disease inflammatory bowel disease GSM7226502 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd IBD patient 2 Laminar propria mononuclear cell cell type: Laminar propria mononuclear cell controlled vocabulary controlled vocabulary disease match: ibd

disease inflammatory bowel disease GSM7226503 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd IBD patient 3 Laminar propria mononuclear cell cell type: Laminar propria mononuclear cell controlled vocabulary controlled vocabulary disease match: ibd

disease inflammatory bowel disease GSM7226504 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd IBD patient 4 Laminar propria mononuclear cell cell type: Laminar propria mononuclear cell controlled vocabulary controlled vocabulary disease match: ibd

organism Homo sapiens GSE230539 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE230539 dataset_title: IPA analysis of CD14-positive monocytes/macrophages from IBD patients and controls organism: Homo sapiens assay_type: microarray proc... keyword match keyword match: homo sapiens

Sample Group Preview

8 rows shown Show Hide

Study totals: Case 4 | Control 4 | Unassigned 0 | Excluded 0 | Ambiguous 0 8 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Inflammatory bowel disease	Case	GSM7226501	IBD patient 1	Laminar propria mononuclear cell Cell type: Laminar propria mononuclear cell	Case marker detected.
Inflammatory bowel disease	Case	GSM7226502	IBD patient 2	Laminar propria mononuclear cell Cell type: Laminar propria mononuclear cell	Case marker detected.
Inflammatory bowel disease	Case	GSM7226503	IBD patient 3	Laminar propria mononuclear cell Cell type: Laminar propria mononuclear cell	Case marker detected.
Inflammatory bowel disease	Case	GSM7226504	IBD patient 4	Laminar propria mononuclear cell Cell type: Laminar propria mononuclear cell	Case marker detected.
Control	Control	GSM7226497	Control 1	Laminar propria mononuclear cell Cell type: Laminar propria mononuclear cell	Sample-local control marker detected.
Control	Control	GSM7226498	Control 2	Laminar propria mononuclear cell Cell type: Laminar propria mononuclear cell	Sample-local control marker detected.
Control	Control	GSM7226499	Control 3	Laminar propria mononuclear cell Cell type: Laminar propria mononuclear cell	Sample-local control marker detected.
Control	Control	GSM7226500	Control 4	Laminar propria mononuclear cell Cell type: Laminar propria mononuclear cell	Sample-local control marker detected.

Use as Discovery Cohort

External Validation Finder

Carry Siftome's disease, organism, specimen, assay, data type, and accession into a validation project. Uncertain fields remain Unknown.