GSE42296

Distinct, non-overlapping gene panels of peripheral blood gene expression predict response to infliximab therapy in rheumatoid arthritis and Crohn's disease

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

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.

Summary

We used microarrays to identify markers predicting responder status in infliximab treatment in 19 rheumatoid arthritis and 20 Crohn's disease patients at week 0 and week 2 of treatment.

Overall design

Peripheral blood samples were obtained at week 0 and week 2 of inxliximab treatment and global gene expression profiling identified markers of responder status.

Source Evidence

4 sources
Source Contribution Status
GEO

Original dataset metadata, sample metadata, source links, and GEO data availability flags.

Sample records
78 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

Primary GEO citations and related PubMed articles that mention this dataset.

2 linked publications 2 DOIs

Primary publication

  1. Peripheral blood derived gene panels predict response to infliximab in rheumatoid arthritis and Crohn's disease. Genome medicine, 2013

Related publications

  1. Integrated Gene Expression Profiling Analysis Reveals Probable Molecular Mechanism and Candidate Biomarker in Anti-TNFα Non-Response IBD Patients. Journal of inflammation research, 2020
Available

Metadata Quality Components

Analysis Readiness

Not ready
55% DE readiness

Contrast completeness

10/25 pts

Only one side of the contrast is present; downstream DE needs both groups.

Minimum group size

0/20 pts

Minimum group size cannot be evaluated until a complete contrast exists.

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

0/10 pts

Critical warnings must be resolved before downstream analysis.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

  • No complete case/control contrast is available.
  • Critical dataset warnings must be resolved.

Next Steps

  • Resolve critical warnings before downstream analysis.

Analysis Preparation Checklist

4/6 ready

Group labels reviewed

Blocked

No complete case/control grouping exists yet.

Review the sample grouping table and assign both case and control groups.

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

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.

Analysis readiness has blockers that must be resolved before DE.

Analysis preparation checklist contains blocked items.

No complete case/control or treatment/control contrast is available.

At least one comparison group has fewer than two samples.

Critical dataset warnings are present.

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

Study design is model-system or unclear and should be reviewed before 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 Crohn's disease, rheumatoid arthritis Disease context came from Normalization rules.
  • Likely case group Crohn's disease 78 samples
  • Likely control group No control group detected 0 samples

Intent Interpretation

  • Downgrade or exclusion reason Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

  • Interpreted disease metadata: Crohn's disease, Rheumatoid arthritis.
  • Processed data is available for downstream review.
  • External evidence: PubMed links 2 publications; 2 DOIs available: PMID 23809696, PMID 32104045.
  • Publication context: Peripheral blood derived gene panels predict response to infliximab in rheumatoid arthritis and Crohn's disease.. Genome medicine, 2013. PMID 23809696. DOI 10.1186/gm463.
  • Publication context: Integrated Gene Expression Profiling Analysis Reveals Probable Molecular Mechanism and Candidate Biomarker in Anti-TNFα Non-Response IBD Patients.. Journal of inflammation research, 2020. PMID 32104045. DOI 10.2147/JIR.S236262.

Cautions

  • 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.
  • Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
  • Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
  • Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
  • Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
  • Missing or unclear metadata. Comparison - Unclear study design. Specimen - Biofluid. 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

Normalized Fields

395 fields

Sample Group Preview

showing 50 of 78 preview rows
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Study totals: Case 78 | Control 0 | Unassigned 0 | Excluded 0 | Ambiguous 0 showing 50 of 78 preview rows
Group Role Accession Title Source / characteristics Reason
Crohn's disease Case GSM1037296 Before treatment (week 0) IBDB14 PBMC Cell type: PBMC; Subject: Patient 1; Response: R - responder; Treatment: Before treatment; Time: Week 0; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037297 Before treatment (week 0) IBDB17 PBMC Cell type: PBMC; Subject: Patient 2; Response: R - responder; Treatment: Before treatment; Time: Week 0; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037298 Before treatment (week 0) IBDB18 PBMC Cell type: PBMC; Subject: Patient 3; Response: R - responder; Treatment: Before treatment; Time: Week 0; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037299 Before treatment (week 0) IBDB22 PBMC Cell type: PBMC; Subject: Patient 4; Response: NR - non-responder; Treatment: Before treatment; Time: Week 0; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037300 Before treatment (week 0) IBDB27 PBMC Cell type: PBMC; Subject: Patient 5; Response: NR - non-responder; Treatment: Before treatment; Time: Week 0; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037301 Before treatment (week 0) IBDB28 PBMC Cell type: PBMC; Subject: Patient 6; Response: R - responder; Treatment: Before treatment; Time: Week 0; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037302 Before treatment (week 0) IBDB33 PBMC Cell type: PBMC; Subject: Patient 7; Response: R - responder; Treatment: Before treatment; Time: Week 0; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037303 Before treatment (week 0) IBDB34 PBMC Cell type: PBMC; Subject: Patient 8; Response: R - responder; Treatment: Before treatment; Time: Week 0; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037304 Before treatment (week 0) IBDB37 PBMC Cell type: PBMC; Subject: Patient 9; Response: R - responder; Treatment: Before treatment; Time: Week 0; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037305 Before treatment (week 0) IBDB40 PBMC Cell type: PBMC; Subject: Patient 10; Response: R - responder; Treatment: Before treatment; Time: Week 0; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037306 Before treatment (week 0) IBDB39 PBMC Cell type: PBMC; Subject: Patient 11; Response: R - responder; Treatment: Before treatment; Time: Week 0; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037307 Before treatment (week 0) IBDB44 PBMC Cell type: PBMC; Subject: Patient 12; Response: NR - non-responder; Treatment: Before treatment; Time: Week 0; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037308 Before treatment (week 0) IBDB42 PBMC Cell type: PBMC; Subject: Patient 13; Response: R - responder; Treatment: Before treatment; Time: Week 0; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037309 Before treatment (week 0) IBDB41 PBMC Cell type: PBMC; Subject: Patient 14; Response: NR - non-responder; Treatment: Before treatment; Time: Week 0; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037310 Before treatment (week 0) IBDB26 PBMC Cell type: PBMC; Subject: Patient 15; Response: R - responder; Treatment: Before treatment; Time: Week 0; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037311 Before treatment (week 0) IBDB23 PBMC Cell type: PBMC; Subject: Patient 16; Response: R - responder; Treatment: Before treatment; Time: Week 0; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037312 Before treatment (week 0) IBDB13 PBMC Cell type: PBMC; Subject: Patient 17; Response: NR - non-responder; Treatment: Before treatment; Time: Week 0; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037313 Before treatment (week 0) IBDB08 PBMC Cell type: PBMC; Subject: Patient 18; Response: R - responder; Treatment: Before treatment; Time: Week 0; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037314 Before treatment (week 0) IBDB03 PBMC Cell type: PBMC; Subject: Patient 19; Response: R - responder; Treatment: Before treatment; Time: Week 0; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037315 Before treatment (week 0) IBDB01 PBMC Cell type: PBMC; Subject: Patient 20; Response: NR - non-responder; Treatment: Before treatment; Time: Week 0; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037316 After treatment (week 2) IBDB16 PBMC Cell type: PBMC; Subject: Patient 1; Response: R - responder; Treatment: Infliximab; Time: Week 2; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037317 After treatment (week 2) IBDB19 PBMC Cell type: PBMC; Subject: Patient 2; Response: R - responder; Treatment: Infliximab; Time: Week 2; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037318 After treatment (week 2) IBDB21 PBMC Cell type: PBMC; Subject: Patient 3; Response: R - responder; Treatment: Infliximab; Time: Week 2; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037319 After treatment (week 2) IBDB24 PBMC Cell type: PBMC; Subject: Patient 4; Response: NR - non-responder; Treatment: Infliximab; Time: Week 2; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037320 After treatment (week 2) IBDB29 PBMC Cell type: PBMC; Subject: Patient 5; Response: NR - non-responder; Treatment: Infliximab; Time: Week 2; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037321 After treatment (week 2) IBDB30 PBMC Cell type: PBMC; Subject: Patient 6; Response: R - responder; Treatment: Infliximab; Time: Week 2; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037322 After treatment (week 2) IBDB35 PBMC Cell type: PBMC; Subject: Patient 7; Response: R - responder; Treatment: Infliximab; Time: Week 2; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037323 After treatment (week 2) IBDB36 PBMC Cell type: PBMC; Subject: Patient 8; Response: R - responder; Treatment: Infliximab; Time: Week 2; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037324 After treatment (week 2) IBDB38 PBMC Cell type: PBMC; Subject: Patient 9; Response: R - responder; Treatment: Infliximab; Time: Week 2; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037325 After treatment (week 2) IBDB43 PBMC Cell type: PBMC; Subject: Patient 10; Response: R - responder; Treatment: Infliximab; Time: Week 2; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037326 After treatment (week 2) IBDB46 PBMC Cell type: PBMC; Subject: Patient 11; Response: R - responder; Treatment: Infliximab; Time: Week 2; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037327 After treatment (week 2) IBDB49 PBMC Cell type: PBMC; Subject: Patient 12; Response: NR - non-responder; Treatment: Infliximab; Time: Week 2; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037328 After treatment (week 2) IBDB47 PBMC Cell type: PBMC; Subject: Patient 13; Response: R - responder; Treatment: Infliximab; Time: Week 2; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037329 After treatment (week 2) IBDB45 PBMC Cell type: PBMC; Subject: Patient 14; Response: NR - non-responder; Treatment: Infliximab; Time: Week 2; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037330 After treatment (week 2) IBDB31 PBMC Cell type: PBMC; Subject: Patient 15; Response: R - responder; Treatment: Infliximab; Time: Week 2; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037331 After treatment (week 2) IBDB25 PBMC Cell type: PBMC; Subject: Patient 16; Response: R - responder; Treatment: Infliximab; Time: Week 2; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037332 After treatment (week 2) IBDB15 PBMC Cell type: PBMC; Subject: Patient 17; Response: NR - non-responder; Treatment: Infliximab; Time: Week 2; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037333 After treatment (week 2) IBDB11 PBMC Cell type: PBMC; Subject: Patient 18; Response: R - responder; Treatment: Infliximab; Time: Week 2; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037334 After treatment (week 2) IBDB05 PBMC Cell type: PBMC; Subject: Patient 19; Response: R - responder; Treatment: Infliximab; Time: Week 2; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1037335 After treatment (week 2) IBDB02 PBMC Cell type: PBMC; Subject: Patient 20; Response: NR - non-responder; Treatment: Infliximab; Time: Week 2; Disease state: Crohn's disease Case marker detected.
Rheumatoid arthritis Case GSM1037336 Before treatment (week 0) RAB07 PBMC Cell type: PBMC; Subject: Patient 1; Response: NR - non-responder; Treatment: Before treatment; Time: Week 0; Disease state: Rheumatoid arthritis Case marker detected.
Rheumatoid arthritis Case GSM1037337 Before treatment (week 0) RAB101 PBMC Cell type: PBMC; Subject: Patient 2; Response: NR - non-responder; Treatment: Before treatment; Time: Week 0; Disease state: Rheumatoid arthritis Case marker detected.
Rheumatoid arthritis Case GSM1037338 Before treatment (week 0) RAB103 PBMC Cell type: PBMC; Subject: Patient 3; Response: NR - non-responder; Treatment: Before treatment; Time: Week 0; Disease state: Rheumatoid arthritis Case marker detected.
Rheumatoid arthritis Case GSM1037339 Before treatment (week 0) RAB104 PBMC Cell type: PBMC; Subject: Patient 4; Response: NR - non-responder; Treatment: Before treatment; Time: Week 0; Disease state: Rheumatoid arthritis Case marker detected.
Rheumatoid arthritis Case GSM1037340 Before treatment (week 0) RAB31 PBMC Cell type: PBMC; Subject: Patient 5; Response: NR - non-responder; Treatment: Before treatment; Time: Week 0; Disease state: Rheumatoid arthritis Case marker detected.
Rheumatoid arthritis Case GSM1037341 Before treatment (week 0) RAB41 PBMC Cell type: PBMC; Subject: Patient 6; Response: NR - non-responder; Treatment: Before treatment; Time: Week 0; Disease state: Rheumatoid arthritis Case marker detected.
Rheumatoid arthritis Case GSM1037342 Before treatment (week 0) RAB63 PBMC Cell type: PBMC; Subject: Patient 7; Response: NR - non-responder; Treatment: Before treatment; Time: Week 0; Disease state: Rheumatoid arthritis Case marker detected.
Rheumatoid arthritis Case GSM1037343 Before treatment (week 0) RAB72 PBMC Cell type: PBMC; Subject: Patient 8; Response: NR - non-responder; Treatment: Before treatment; Time: Week 0; Disease state: Rheumatoid arthritis Case marker detected.
Rheumatoid arthritis Case GSM1037344 Before treatment (week 0) RAB83 PBMC Cell type: PBMC; Subject: Patient 9; Response: NR - non-responder; Treatment: Before treatment; Time: Week 0; Disease state: Rheumatoid arthritis Case marker detected.
Rheumatoid arthritis Case GSM1037345 Before treatment (week 0) RAB90 PBMC Cell type: PBMC; Subject: Patient 10; Response: NR - non-responder; Treatment: Before treatment; Time: Week 0; Disease state: Rheumatoid arthritis Case marker detected.
28 additional case samples are hidden from this preview.

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