GSE186963

Whole blood gene expression from infliximab treated Crohn's disease patients at three time points: pre-treatment, two weeks and fourteen weeks post first treatment

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

Personalized treatment of complex diseases is an unmet medical need pushing towards drug biomarker identification of one drug-disease combination at a time. Here, we used a novel computational approach for modeling cell-centered individual-level network dynamics from high-dimensional blood data to predict infliximab response and uncover individual variation of non-response. We identified and validated that the RAC1-PAK1 axis is predictive of infliximab response in inflammatory bowel disease. Intermediate monocytes, which closely correlated with inflammation state, play a key role in the RAC1-PAK1 responses, supporting their modulation as a therapeutic target. This axis also predicts response in Rheumatoid arthritis, validated in three public cohorts. Our findings support pan-disease drug response diagnostics from blood, implicating common mechanisms of drug response or failure across diseases.

Overall design

Whole blood samples from anti-TNF responding (n=15) and non-responding (n=9) IBD patients at three time points: pre-treatment, two weeks and fourteen weeks post first treatment

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
72 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

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, inflammatory bowel disease, rheumatoid arthritis Disease context came from Normalization rules.
  • Likely case group Crohn's disease 72 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, Inflammatory bowel disease, Rheumatoid arthritis.
  • Processed data is available for downstream review.

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.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • 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

318 fields

Sample Group Preview

showing 50 of 72 preview rows
Show Hide
Study totals: Case 72 | Control 0 | Unassigned 0 | Excluded 0 | Ambiguous 0 showing 50 of 72 preview rows
Group Role Accession Title Source / characteristics Reason
Crohn's disease Case GSM5664373 HR_38_V1 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-38; Response status: Non-responder; Visit: Baseline; Crp: 2.1 Case marker detected.
Crohn's disease Case GSM5664374 HR_38_V2 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-38; Response status: Non-responder; Visit: W2; Crp: 1.2 Case marker detected.
Crohn's disease Case GSM5664375 HR_38_V3 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-38; Response status: Non-responder; Visit: W14; Crp: 2 Case marker detected.
Crohn's disease Case GSM5664376 HR_39_V1 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-39; Response status: Responder; Visit: Baseline; Crp: 2.6 Case marker detected.
Crohn's disease Case GSM5664377 HR_39_V2 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-39; Response status: Responder; Visit: W2; Crp: 0.1 Case marker detected.
Crohn's disease Case GSM5664378 HR_39_V3 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-39; Response status: Responder; Visit: W14; Crp: 0.4 Case marker detected.
Crohn's disease Case GSM5664379 HR_40_V1 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-40; Response status: Responder; Visit: Baseline; Crp: 1 Case marker detected.
Crohn's disease Case GSM5664380 HR_40_V2 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-40; Response status: Responder; Visit: W2; Crp: 1.1 Case marker detected.
Crohn's disease Case GSM5664381 HR_40_V3 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-40; Response status: Responder; Visit: W14; Crp: 2.67 Case marker detected.
Crohn's disease Case GSM5664382 HR_42_V1 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-42; Response status: Responder; Visit: Baseline; Crp: 3.4 Case marker detected.
Crohn's disease Case GSM5664383 HR_42_V2 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-42; Response status: Responder; Visit: W2; Crp: 0.9 Case marker detected.
Crohn's disease Case GSM5664384 HR_42_V3 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-42; Response status: Responder; Visit: W14; Crp: 0.48 Case marker detected.
Crohn's disease Case GSM5664385 HR_44_V1 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-44; Response status: Responder; Visit: Baseline; Crp: 19.6 Case marker detected.
Crohn's disease Case GSM5664386 HR_44_V2 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-44; Response status: Responder; Visit: W2; Crp: 2.1 Case marker detected.
Crohn's disease Case GSM5664387 HR_44_V3 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-44; Response status: Responder; Visit: W14; Crp: 1.19 Case marker detected.
Crohn's disease Case GSM5664388 HR_46_V1 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-46; Response status: Responder; Visit: Baseline; Crp: 6.8 Case marker detected.
Crohn's disease Case GSM5664389 HR_46_V2 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-46; Response status: Responder; Visit: W2; Crp: 3.22 Case marker detected.
Crohn's disease Case GSM5664390 HR_46_V3 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-46; Response status: Responder; Visit: W14; Crp: 3 Case marker detected.
Crohn's disease Case GSM5664391 HR_47_V1 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-47; Response status: Responder; Visit: Baseline; Crp: 125.7 Case marker detected.
Crohn's disease Case GSM5664392 HR_47_V2 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-47; Response status: Responder; Visit: W2; Crp: 2.7 Case marker detected.
Crohn's disease Case GSM5664393 HR_47_V3 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-47; Response status: Responder; Visit: W14; Crp: 24.2 Case marker detected.
Crohn's disease Case GSM5664394 HR_48_V1 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-48; Response status: Responder; Visit: Baseline; Crp: 1.8 Case marker detected.
Crohn's disease Case GSM5664395 HR_48_V2 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-48; Response status: Responder; Visit: W2; Crp: 0.8 Case marker detected.
Crohn's disease Case GSM5664396 HR_48_V3 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-48; Response status: Responder; Visit: W14; Crp: 1 Case marker detected.
Crohn's disease Case GSM5664397 HR_29_V1 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-29; Response status: Responder; Visit: Baseline; Crp: 4.9 Case marker detected.
Crohn's disease Case GSM5664398 HR_29_V2 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-29; Response status: Responder; Visit: W2; Crp: 2.5 Case marker detected.
Crohn's disease Case GSM5664399 HR_29_V3 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-29; Response status: Responder; Visit: W14; Crp: 1.15 Case marker detected.
Crohn's disease Case GSM5664400 HR_30_V1 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-30; Response status: Non-responder; Visit: Baseline; Crp: 15.8 Case marker detected.
Crohn's disease Case GSM5664401 HR_30_V2 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-30; Response status: Non-responder; Visit: W2; Crp: 4.78 Case marker detected.
Crohn's disease Case GSM5664402 HR_30_V3 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-30; Response status: Non-responder; Visit: W14; Crp: 43.6 Case marker detected.
Crohn's disease Case GSM5664403 HR_31_V1 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-31; Response status: Responder; Visit: Baseline; Crp: 44 Case marker detected.
Crohn's disease Case GSM5664404 HR_31_V2 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-31; Response status: Responder; Visit: W2; Crp: 5.43 Case marker detected.
Crohn's disease Case GSM5664405 HR_31_V3 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-31; Response status: Responder; Visit: W14; Crp: 5.9 Case marker detected.
Crohn's disease Case GSM5664406 HR_32_V1 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-32; Response status: Non-responder; Visit: Baseline; Crp: 16.5 Case marker detected.
Crohn's disease Case GSM5664407 HR_32_V2 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-32; Response status: Non-responder; Visit: W2; Crp: 3.8 Case marker detected.
Crohn's disease Case GSM5664408 HR_32_V3 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-32; Response status: Non-responder; Visit: W14; Crp: 7 Case marker detected.
Crohn's disease Case GSM5664409 HR_33_V1 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-33; Response status: Responder; Visit: Baseline; Crp: 21.17 Case marker detected.
Crohn's disease Case GSM5664410 HR_33_V2 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-33; Response status: Responder; Visit: W2; Crp: 1.75 Case marker detected.
Crohn's disease Case GSM5664411 HR_33_V3 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-33; Response status: Responder; Visit: W14; Crp: 9.81 Case marker detected.
Crohn's disease Case GSM5664412 HR_35_V1 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-35; Response status: Responder; Visit: Baseline; Crp: 27.18 Case marker detected.
Crohn's disease Case GSM5664413 HR_35_V2 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-35; Response status: Responder; Visit: W2; Crp: 11.22 Case marker detected.
Crohn's disease Case GSM5664414 HR_35_V3 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-35; Response status: Responder; Visit: W14; Crp: 18.3 Case marker detected.
Crohn's disease Case GSM5664415 HR_36_V1 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-36; Response status: Non-responder; Visit: Baseline; Crp: 82.7 Case marker detected.
Crohn's disease Case GSM5664416 HR_36_V2 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-36; Response status: Non-responder; Visit: W2; Crp: 23.7 Case marker detected.
Crohn's disease Case GSM5664417 HR_36_V3 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-36; Response status: Non-responder; Visit: W14; Crp: 116 Case marker detected.
Crohn's disease Case GSM5664418 HR_37_V1 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-37; Response status: Non-responder; Visit: Baseline; Crp: 4.26 Case marker detected.
Crohn's disease Case GSM5664419 HR_37_V2 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-37; Response status: Non-responder; Visit: W2; Crp: 2 Case marker detected.
Crohn's disease Case GSM5664420 HR_37_V3 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-37; Response status: Non-responder; Visit: W14; Crp: 7.7 Case marker detected.
Crohn's disease Case GSM5664421 HR_20_V1 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-20; Response status: Responder; Visit: Baseline; Crp: 15.6 Case marker detected.
Crohn's disease Case GSM5664422 HR_20_V2 Whole blood Disease: Crohn's disease; Treatment: Infliximab; Patient: HR-20; Response status: Responder; Visit: W2; Crp: NA Case marker detected.
22 additional case samples are hidden from this preview.

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.