GSE92472

Expression of long non-coding RNAs in autoimmunity and linkage to enhancer function and autoimmune disease risk genetic variants

Whole-study status Exploratory only

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

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

Selected cohort requirements

Samples meeting selected requirements: 0 cases / 0 controls

View matching samples

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: bulk RNA-seq
Organism: Homo sapiens
Whole-study samples: 15 samples
Specimen: Biofluid
Reported/interpreted study design: Patient biofluid vs healthy control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Spurlock CF, Aune TM, Spurlock III CF
Contact name: Charles F Spurlock III
Submission date: 2016-12-15
Last update: 2019-08-28
Organization: Vanderbilt University School of Medicine
Department: Medicine
Public date: 2017-04-11
Experiment types: Expression profiling by high throughput sequencing
Platforms: GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Series type: Series
SubSeries: Not available
BioProject: PRJNA357628

Summary

Genome-wide association studies have identified numerous genetic variants conferring autoimmune disease risk. Most of these genetic variants lie outside protein-coding genes hampering mechanistic explorations. Numerous mRNAs are also differentially expressed in autoimmune disease but their regulation is also unclear. The majority of the human genome is transcribed yet its biologic significance is incompletely understood. We performed whole genome RNA-sequencing [RNA-seq] to categorize expression of mRNAs, known and novel long non-coding RNAs [lncRNAs] in leukocytes from subjects with autoimmune disease and identified annotated and novel lncRNAs differentially expressed across multiple disorders. We found that loci transcribing novel lncRNAs were not randomly distributed across the genome but co-localized with leukocyte transcriptional enhancers, especially super-enhancers, and near genetic variants associated with autoimmune disease risk. We propose that alterations in enhancer function, including lncRNA expression, produced by genetics and environment, change cellular phenotypes contributing to disease risk and pathogenesis and represent attractive therapeutic targets.

Overall design

We extracted RNA from peripheral whole blood across healthy control and disease subjects.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 15 GSM samples	Primary source
recount3	Trusted source evidence for processed count availability. recount3 project ID srp095209	Available
Expression Atlas	Planned source for curated expression experiment links.	No match found
PubMed	Primary GEO citations and related PubMed articles that mention this dataset. 1 linked publication 1 DOI Primary publication Expression of long non-coding RNAs in autoimmunity and linkage to enhancer function and autoimmune disease risk genetic variants. Journal of autoimmunity, 2017 PubMed DOI	Available

Metadata Quality Components

Persisted metadata quality

100 pts

Clarity: 100%
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: Anatomical source metadata 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

Review before analysis

76% DE readiness

Contrast completeness

25/25 pts

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

Minimum group size

8/20 pts

A contrast exists, but at least one group is below the minimum sample count.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

3/15 pts

Unassigned or review-needed samples remain before analysis.

Blocking warnings

10/10 pts

No dataset warnings are present.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

At least one contrast group is below the minimum sample count.
10 samples are still unassigned.

Next Steps

Resolve unassigned or review-needed samples in the grouping table.

Analysis Preparation Checklist

3/6 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

Blocked

At least one group has fewer than 2 samples.

Choose a larger dataset or merge only scientifically valid groups.

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

Needs review

0 review-needed samples and 10 unassigned samples remain.

Resolve ambiguous and unassigned samples before finalizing the contrast.

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.

Analysis readiness has blockers that must be resolved before DE.

Analysis preparation checklist contains blocked items.

At least one comparison group has fewer than two samples.

One or more samples are unassigned and need manual grouping decisions.

Why This Is Ranked Here

Tumor vs normal

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

Applied Review Decisions

No active review decisions affect this ranking.

Derived Classifications

Disease context Crohn's disease, lupus erythematosus, sjogren syndrome, systemic lupus erythematosus, ulcerative colitis Disease context came from Normalization rules.
Likely case group Ulcerative colitis 4 samples
Likely control group Healthy control 1 samples

Intent Interpretation

Downgrade or exclusion reason Downgraded for tissue search because it is a biofluid cohort. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 20%.
Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Crohn's disease, Lupus erythematosus, Sjogren syndrome, Systemic lupus erythematosus, Ulcerative colitis.
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 28420548.
Publication context: Expression of long non-coding RNAs in autoimmunity and linkage to enhancer function and autoimmune disease risk genetic variants.. Journal of autoimmunity, 2017. PMID 28420548. DOI 10.1016/j.jaut.2017.03.014.

Cautions

Downgraded for tissue search because it is a biofluid cohort.
Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
Overall score capped because comparison suitability is weak for the selected search intent.
Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

No dataset warnings

Normalized Fields

71 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source blood GSM2430372 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood source_name: peripheral whole blood draw sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2430373 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood source_name: peripheral whole blood draw sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2430374 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood source_name: peripheral whole blood draw sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2430375 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood source_name: peripheral whole blood draw sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2430376 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood source_name: peripheral whole blood draw sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2430377 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood source_name: peripheral whole blood draw sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2430378 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood source_name: peripheral whole blood draw sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2430379 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood source_name: peripheral whole blood draw sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2430380 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood source_name: peripheral whole blood draw sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2430381 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood source_name: peripheral whole blood draw sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2430382 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood source_name: peripheral whole blood draw sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2430383 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood source_name: peripheral whole blood draw sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2430384 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood source_name: peripheral whole blood draw sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2430385 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood source_name: peripheral whole blood draw sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2430386 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood source_name: peripheral whole blood draw sample-anatomical-source-v1 sample-local anatomical source

assay_type bulk RNA-seq GSE92472 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence bulk rna-seq dataset_accession: GSE92472 dataset_title: Expression of long non-coding RNAs in autoimmunity and linkage to enhancer function and autoimmune disease risk genetic variants organ... keyword match keyword match: bulk rna-seq

collection_method venipuncture GSM2430372 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood draw Ulcerative colitis peripheral whole blood draw type: Ulcerative colitis controlled vocabulary controlled vocabulary collection method match: blood draw

collection_method venipuncture GSM2430373 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood draw Crohn's disease peripheral whole blood draw type: Crohn's disease controlled vocabulary controlled vocabulary collection method match: blood draw

collection_method venipuncture GSM2430374 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood draw Irritable bowel syndrome peripheral whole blood draw type: Irritable bowel syndrome controlled vocabulary controlled vocabulary collection method match: blood draw

collection_method venipuncture GSM2430375 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood draw Celiac disease peripheral whole blood draw type: Celiac disease controlled vocabulary controlled vocabulary collection method match: blood draw

collection_method venipuncture GSM2430376 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood draw Fibromyalgia syndrome peripheral whole blood draw type: Fibromyalgia syndrome controlled vocabulary controlled vocabulary collection method match: blood draw

collection_method venipuncture GSM2430377 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood draw CIS-MS peripheral whole blood draw type: CIS-MS controlled vocabulary controlled vocabulary collection method match: blood draw

collection_method venipuncture GSM2430378 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood draw MS-NAÏVE peripheral whole blood draw type: MS-NAIVE controlled vocabulary controlled vocabulary collection method match: blood draw

collection_method venipuncture GSM2430379 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood draw MS-EST peripheral whole blood draw type: MS-EST controlled vocabulary controlled vocabulary collection method match: blood draw

collection_method venipuncture GSM2430380 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood draw Healthy control subject peripheral whole blood draw type: Healthy control subject controlled vocabulary controlled vocabulary collection method match: blood draw

collection_method venipuncture GSM2430381 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood draw RA-MTX (not receiving methotrexate) peripheral whole blood draw type: RA-MTX (not receiving methotrexate) controlled vocabulary controlled vocabulary collection method match: blood draw

collection_method venipuncture GSM2430382 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood draw RA+MTX (receiving methotrexate) peripheral whole blood draw type: RA+MTX (receiving methotrexate) controlled vocabulary controlled vocabulary collection method match: blood draw

collection_method venipuncture GSM2430383 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood draw Systemic lupus erythematosus peripheral whole blood draw type: Systemic lupus erythematosus controlled vocabulary controlled vocabulary collection method match: blood draw

collection_method venipuncture GSM2430384 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood draw Psoriasis peripheral whole blood draw type: Psoriasis controlled vocabulary controlled vocabulary collection method match: blood draw

collection_method venipuncture GSM2430385 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood draw Psoriatic arthritis peripheral whole blood draw type: Psoriatic arthritis controlled vocabulary controlled vocabulary collection method match: blood draw

collection_method venipuncture GSM2430386 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood draw Sjogren's syndrome peripheral whole blood draw type: Sjogren's syndrome controlled vocabulary controlled vocabulary collection method match: blood draw

control_type healthy control GSM2430380 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Healthy control subject peripheral whole blood draw type: Healthy control subject controlled vocabulary controlled vocabulary control type match: healthy control

disease ulcerative colitis GSM2430372 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Ulcerative colitis peripheral whole blood draw type: Ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease Crohn's disease GSM2430373 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Crohn's disease peripheral whole blood draw type: Crohn's disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease lupus erythematosus GSM2430383 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence lupus erythematosus Systemic lupus erythematosus peripheral whole blood draw type: Systemic lupus erythematosus controlled vocabulary controlled vocabulary disease match: lupus erythematosus

disease systemic lupus erythematosus GSM2430383 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence systemic lupus erythematosus Systemic lupus erythematosus peripheral whole blood draw type: Systemic lupus erythematosus controlled vocabulary controlled vocabulary disease match: systemic lupus erythematosus

disease sjogren syndrome GSM2430386 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence sjogren s syndrome Sjogren's syndrome peripheral whole blood draw type: Sjogren's syndrome controlled vocabulary controlled vocabulary disease match: sjogren s syndrome

normal_tissue_type healthy donor tissue GSM2430380 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Healthy control subject peripheral whole blood draw type: Healthy control subject controlled vocabulary controlled vocabulary normal tissue type match: healthy control

organism Homo sapiens GSE92472 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE92472 dataset_title: Expression of long non-coding RNAs in autoimmunity and linkage to enhancer function and autoimmune disease risk genetic variants organ... keyword match keyword match: homo sapiens

sample_type normal tissue GSM2430380 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Healthy control subject peripheral whole blood draw type: Healthy control subject controlled vocabulary controlled vocabulary sample type match: healthy control

specimen_material whole blood GSM2430372 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood Ulcerative colitis peripheral whole blood draw type: Ulcerative colitis controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM2430373 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood Crohn's disease peripheral whole blood draw type: Crohn's disease controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM2430374 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood Irritable bowel syndrome peripheral whole blood draw type: Irritable bowel syndrome controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM2430375 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood Celiac disease peripheral whole blood draw type: Celiac disease controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM2430376 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood Fibromyalgia syndrome peripheral whole blood draw type: Fibromyalgia syndrome controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM2430377 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood CIS-MS peripheral whole blood draw type: CIS-MS controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM2430378 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood MS-NAÏVE peripheral whole blood draw type: MS-NAIVE controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM2430379 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood MS-EST peripheral whole blood draw type: MS-EST controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM2430380 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood Healthy control subject peripheral whole blood draw type: Healthy control subject controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM2430381 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood RA-MTX (not receiving methotrexate) peripheral whole blood draw type: RA-MTX (not receiving methotrexate) controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM2430382 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood RA+MTX (receiving methotrexate) peripheral whole blood draw type: RA+MTX (receiving methotrexate) controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM2430383 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood Systemic lupus erythematosus peripheral whole blood draw type: Systemic lupus erythematosus controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM2430384 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood Psoriasis peripheral whole blood draw type: Psoriasis controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM2430385 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood Psoriatic arthritis peripheral whole blood draw type: Psoriatic arthritis controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM2430386 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood Sjogren's syndrome peripheral whole blood draw type: Sjogren's syndrome controlled vocabulary controlled vocabulary specimen material match: whole blood

tissue blood GSE92472 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood dataset_accession: GSE92472 dataset_title: Expression of long non-coding RNAs in autoimmunity and linkage to enhancer function and autoimmune disease risk genetic variants organ... controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2430372 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Ulcerative colitis peripheral whole blood draw type: Ulcerative colitis controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2430373 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Crohn's disease peripheral whole blood draw type: Crohn's disease controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2430374 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Irritable bowel syndrome peripheral whole blood draw type: Irritable bowel syndrome controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2430375 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Celiac disease peripheral whole blood draw type: Celiac disease controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2430376 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Fibromyalgia syndrome peripheral whole blood draw type: Fibromyalgia syndrome controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2430377 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood CIS-MS peripheral whole blood draw type: CIS-MS controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2430378 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood MS-NAÏVE peripheral whole blood draw type: MS-NAIVE controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2430379 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood MS-EST peripheral whole blood draw type: MS-EST controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2430380 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Healthy control subject peripheral whole blood draw type: Healthy control subject controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2430381 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood RA-MTX (not receiving methotrexate) peripheral whole blood draw type: RA-MTX (not receiving methotrexate) controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2430382 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood RA+MTX (receiving methotrexate) peripheral whole blood draw type: RA+MTX (receiving methotrexate) controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2430383 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Systemic lupus erythematosus peripheral whole blood draw type: Systemic lupus erythematosus controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2430384 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Psoriasis peripheral whole blood draw type: Psoriasis controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2430385 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Psoriatic arthritis peripheral whole blood draw type: Psoriatic arthritis controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2430386 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Sjogren's syndrome peripheral whole blood draw type: Sjogren's syndrome controlled vocabulary controlled vocabulary tissue match: blood

Sample Group Preview

15 rows shown Show Hide

Study totals: Case 4 | Control 1 | Unassigned 10 | Excluded 0 | Ambiguous 0 15 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Ulcerative colitis	Case	GSM2430372	Ulcerative colitis	Peripheral whole blood draw Type: Ulcerative colitis	Case marker detected.
Crohn's disease	Case	GSM2430373	Crohn's disease	Peripheral whole blood draw Type: Crohn's disease	Case marker detected.
Systemic lupus erythematosus	Case	GSM2430383	Systemic lupus erythematosus	Peripheral whole blood draw Type: Systemic lupus erythematosus	Case marker detected.
Sjogren syndrome	Case	GSM2430386	Sjogren's syndrome	Peripheral whole blood draw Type: Sjogren's syndrome	Case marker detected.
Healthy control	Control	GSM2430380	Healthy control subject	Peripheral whole blood draw Type: Healthy control subject	Sample-local control marker detected.
Unassigned	Unassigned	GSM2430374	Irritable bowel syndrome	Peripheral whole blood draw Type: Irritable bowel syndrome	No explicit case or control marker detected.
Unassigned	Unassigned	GSM2430375	Celiac disease	Peripheral whole blood draw Type: Celiac disease	No explicit case or control marker detected.
Unassigned	Unassigned	GSM2430376	Fibromyalgia syndrome	Peripheral whole blood draw Type: Fibromyalgia syndrome	No explicit case or control marker detected.
Unassigned	Unassigned	GSM2430377	CIS-MS	Peripheral whole blood draw Type: CIS-MS	No explicit case or control marker detected.
Unassigned	Unassigned	GSM2430378	MS-NAÏVE	Peripheral whole blood draw Type: MS-NAIVE	No explicit case or control marker detected.
Unassigned	Unassigned	GSM2430379	MS-EST	Peripheral whole blood draw Type: MS-EST	No explicit case or control marker detected.
Unassigned	Unassigned	GSM2430381	RA-MTX (not receiving methotrexate)	Peripheral whole blood draw Type: RA-MTX (not receiving methotrexate)	No explicit case or control marker detected.
Unassigned	Unassigned	GSM2430382	RA+MTX (receiving methotrexate)	Peripheral whole blood draw Type: RA+MTX (receiving methotrexate)	No explicit case or control marker detected.
Unassigned	Unassigned	GSM2430384	Psoriasis	Peripheral whole blood draw Type: Psoriasis	No explicit case or control marker detected.
Unassigned	Unassigned	GSM2430385	Psoriatic arthritis	Peripheral whole blood draw Type: Psoriatic arthritis	No explicit case or 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.

Summary

Overall design

Source Evidence

Primary publication

Metadata Quality Components

Analysis Readiness

Blockers

Next Steps

Analysis Preparation Checklist

Bioinformatician Review

Why This Is Ranked Here

Applied Review Decisions

Derived Classifications

Intent Interpretation

Ranking Facts

Supporting evidence

Cautions

Dataset Warnings

Normalized Fields

Sample Group Preview

Use as Discovery Cohort