GSE191328

Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease [RNA-Seq]

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

112 case / 25 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
bulk RNA-seq
Organism
Homo sapiens
Whole-study samples
201 samples
Specimen
Biofluid
Reported/interpreted study design
Disease/model vs control Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Mishra N, Aden K, Baran N, Rosentiel P
Contact name
Neha Mishra
Submission date
2021-12-20
Last update
2024-12-13
Organization
Institute of Clinical Molecular Biology
Department
Cell biology Lab
Public date
2022-07-26
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA790985

Summary

We investigated the dynamics of gene expression in blood samples of IBD patients treated with infliximab and vedolizumab and analyzed the predictive potential regarding therapy outcome.

Overall design

We performed a longitudinal, blood-based multi-omics study in two prospective IBD patient cohorts receiving first time infliximab therapy (discovery: 14 patients, replication: 23 patients) and one prospective IBD patient cohort receiving first time vedolizumab therapy (17 patients). Samples were collected at up to 7 timepoints (from baseline to 14 weeks after therapy induction).

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
201 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.

4 linked publications 4 DOIs

Primary publication

  1. Hexokinase 2 expression in apical enterocytes correlates with inflammation severity in patients with inflammatory bowel disease. BMC medicine, 2024
  2. Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease. Genome medicine, 2022
  3. The SYSCID map: a graphical and computational resource of molecular mechanisms across rheumatoid arthritis, systemic lupus erythematosus and inflammatory bowel disease. Frontiers in immunology, 2023

Related publications

  1. Identification of S100A9 as a target for diagnosis and treatment of Crohn's Disease after Vedolizumab treatment failure. Immunology letters, 2025
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: Treatment status metadata normalized where treatment is part of the comparison. 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
85% 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

3/15 pts

Unassigned or review-needed samples remain before analysis.

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

  • 64 samples are still unassigned.

Next Steps

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

Analysis Preparation Checklist

4/6 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

Needs review

0 review-needed samples and 64 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.

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

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

  • Disease context Inflammatory bowel disease, ulcerative colitis Disease context came from Normalization rules.
  • Likely case group Ulcerative colitis 112 samples
  • Likely control group Untreated 25 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: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Interpreted disease metadata: Inflammatory bowel disease, Ulcerative colitis.
  • Processed data is available for downstream review.
  • External evidence: PubMed links 4 publications; 4 DOIs available: PMID 36153599, PMID 38022524, PMID 39444028, PMID 40280281.
  • Publication context: Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease.. Genome medicine, 2022. PMID 36153599. DOI 10.1186/s13073-022-01112-z.
  • Publication context: The SYSCID map: a graphical and computational resource of molecular mechanisms across rheumatoid arthritis, systemic lupus erythematosus and inflammatory bowel disease.. Frontiers in immunology, 2023. PMID 38022524. DOI 10.3389/fimmu.2023.1257321.
  • Publication context: Hexokinase 2 expression in apical enterocytes correlates with inflammation severity in patients with inflammatory bowel disease.. BMC medicine, 2024. PMID 39444028. DOI 10.1186/s12916-024-03710-7.
  • Publication context: 1 additional linked PubMed publications are available.

Cautions

  • Downgraded for tissue search because it is a biofluid cohort.
  • Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
  • 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

Normalized Fields

showing 500 of 571 fields

Sample Group Preview

showing 125 of 201 preview rows Show Hide
Study totals: Case 112 | Control 25 | Unassigned 64 | Excluded 0 | Ambiguous 0 showing 125 of 201 preview rows
Group Role Accession Title Source / characteristics Reason
Ulcerative colitis Case GSM5743705 28_6w_IFX_NR_RNA Peripheral Whole-Blood Patient: 28; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 6w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743706 28_14w_IFX_NR_RNA Peripheral Whole-Blood Patient: 28; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 14w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743707 29_baseline_IFX_NR_RNA Peripheral Whole-Blood Patient: 29; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: Baseline; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743708 29_2w_IFX_NR_RNA Peripheral Whole-Blood Patient: 29; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 2w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743709 29_6w_IFX_NR_RNA Peripheral Whole-Blood Patient: 29; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 6w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743710 29_14w_IFX_NR_RNA Peripheral Whole-Blood Patient: 29; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 14w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743711 23_6w_IFX_NR_RNA Peripheral Whole-Blood Patient: 23; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 6w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743713 23_14w_IFX_NR_RNA Peripheral Whole-Blood Patient: 23; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 14w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743715 24_baseline_IFX_NR_RNA Peripheral Whole-Blood Patient: 24; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: Baseline; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743717 24_2w_IFX_NR_RNA Peripheral Whole-Blood Patient: 24; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 2w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743719 24_6w_IFX_NR_RNA Peripheral Whole-Blood Patient: 24; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 6w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743720 24_14w_IFX_NR_RNA Peripheral Whole-Blood Patient: 24; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 14w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743723 15_baseline_IFX_R_RNA Peripheral Whole-Blood Patient: 15; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: Baseline; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743724 12_baseline_IFX_R_RNA Peripheral Whole-Blood Patient: 12; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: Baseline; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743725 15_2w_IFX_R_RNA Peripheral Whole-Blood Patient: 15; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 2w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743726 12_2w_IFX_R_RNA Peripheral Whole-Blood Patient: 12; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 2w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743727 15_6w_IFX_R_RNA Peripheral Whole-Blood Patient: 15; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 6w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743728 12_6w_IFX_R_RNA Peripheral Whole-Blood Patient: 12; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 6w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743729 28_baseline_IFX_NR_RNA Peripheral Whole-Blood Patient: 28; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: Baseline; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743730 23_baseline_IFX_NR_RNA Peripheral Whole-Blood Patient: 23; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: Baseline; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743731 15_14w_IFX_R_RNA Peripheral Whole-Blood Patient: 15; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 14w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743732 12_14w_IFX_R_RNA Peripheral Whole-Blood Patient: 12; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 14w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743733 28_2w_IFX_NR_RNA Peripheral Whole-Blood Patient: 28; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 2w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743734 23_2w_IFX_NR_RNA Peripheral Whole-Blood Patient: 23; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 2w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743738 12_4h_IFX_R_RNA Peripheral Whole-Blood Patient: 12; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 4h; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743740 12_24h_IFX_R_RNA Peripheral Whole-Blood Patient: 12; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 24h; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743741 39_baseline_IFX_NR_RNA Peripheral Whole-Blood Patient: 39; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: Baseline; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743742 12_72h_IFX_R_RNA Peripheral Whole-Blood Patient: 12; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 72h; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743743 39_2w_IFX_NR_RNA Peripheral Whole-Blood Patient: 39; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 2w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743745 43_baseline_IFX_R_RNA Peripheral Whole-Blood Patient: 43; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: Baseline; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743746 39_6w_IFX_NR_RNA Peripheral Whole-Blood Patient: 39; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 6w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743748 43_2w_IFX_R_RNA Peripheral Whole-Blood Patient: 43; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 2w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743749 23_4h_IFX_NR_RNA Peripheral Whole-Blood Patient: 23; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 4h; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743750 39_14w_IFX_NR_RNA Peripheral Whole-Blood Patient: 39; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 14w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743752 43_6w_IFX_R_RNA Peripheral Whole-Blood Patient: 43; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 6w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743753 23_24h_IFX_NR_RNA Peripheral Whole-Blood Patient: 23; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 24h; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743756 43_14w_IFX_R_RNA Peripheral Whole-Blood Patient: 43; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 14w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743757 23_72h_IFX_NR_RNA Peripheral Whole-Blood Patient: 23; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 72h; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743760 44_baseline_IFX_NR_RNA Peripheral Whole-Blood Patient: 44; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: Baseline; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743762 44_6w_IFX_NR_RNA Peripheral Whole-Blood Patient: 44; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 6w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743763 44_14w_IFX_NR_RNA Peripheral Whole-Blood Patient: 44; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 14w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743764 29_4h_IFX_NR_RNA Peripheral Whole-Blood Patient: 29; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 4h; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743766 29_24h_IFX_NR_RNA Peripheral Whole-Blood Patient: 29; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 24h; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743767 29_72h_IFX_NR_RNA Peripheral Whole-Blood Patient: 29; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 72h; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743770 5_6w_VDZ_R_RNA Peripheral Whole-Blood Patient: 5; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Remission; Time point: 6w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743772 5_14w_VDZ_R_RNA Peripheral Whole-Blood Patient: 5; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Remission; Time point: 14w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743777 4_baseline_VDZ_R_RNA Peripheral Whole-Blood Patient: 4; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Remission; Time point: Baseline; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743779 4_2w_VDZ_R_RNA Peripheral Whole-Blood Patient: 4; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Remission; Time point: 2w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743781 4_6w_VDZ_R_RNA Peripheral Whole-Blood Patient: 4; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Remission; Time point: 6w; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM5743782 8_baseline_VDZ_NR_RNA Peripheral Whole-Blood Patient: 8; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Non-remission; Time point: Baseline; Diagnosis: UC Case marker detected.
62 additional case samples are hidden from this preview.
Untreated Control GSM5743718 14_baseline_IFX_R_RNA Peripheral Whole-Blood Patient: 14; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743735 13_baseline_IFX_R_RNA Peripheral Whole-Blood Patient: 13; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743754 40_baseline_IFX_R_RNA Peripheral Whole-Blood Patient: 40; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743765 38_baseline_IFX_NR_RNA Peripheral Whole-Blood Patient: 38; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743769 3_baseline_VDZ_NR_RNA Peripheral Whole-Blood Patient: 3; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Non-remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743774 7_baseline_VDZ_R_RNA Peripheral Whole-Blood Patient: 7; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743801 26_baseline_VDZ_NR_RNA Peripheral Whole-Blood Patient: 26; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Non-remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743803 19_baseline_VDZ_NR_RNA Peripheral Whole-Blood Patient: 19; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Non-remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743814 25_baseline_VDZ_R_RNA Peripheral Whole-Blood Patient: 25; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743818 41_baseline_VDZ_NR_RNA Peripheral Whole-Blood Patient: 41; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Non-remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743830 31_baseline_VDZ_R_RNA Peripheral Whole-Blood Patient: 31; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743846 RC_055_baseline_IFX_R_RNA Peripheral Whole-Blood Patient: RC_055; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743848 RC_144_baseline_IFX_R_RNA Peripheral Whole-Blood Patient: RC_144; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743856 RC_010_baseline_IFX_NR_RNA Peripheral Whole-Blood Patient: RC_010; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743857 RC_116_baseline_IFX_R_RNA Peripheral Whole-Blood Patient: RC_116; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743858 RC_060_baseline_IFX_NR_RNA Peripheral Whole-Blood Patient: RC_060; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743867 RC_022_baseline_IFX_R_RNA Peripheral Whole-Blood Patient: RC_022; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743882 RC_162_baseline_IFX_NR_RNA Peripheral Whole-Blood Patient: RC_162; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743885 RC_142_baseline_IFX_R_RNA Peripheral Whole-Blood Patient: RC_142; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743887 RC_161_baseline_IFX_NR_RNA Peripheral Whole-Blood Patient: RC_161; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743889 RC_004_baseline_IFX_NR_RNA Peripheral Whole-Blood Patient: RC_004; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743891 RC_012_baseline_IFX_R_RNA Peripheral Whole-Blood Patient: RC_012; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743892 RC_140_baseline_IFX_R_RNA Peripheral Whole-Blood Patient: RC_140; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743894 RC_036_baseline_IFX_R_RNA Peripheral Whole-Blood Patient: RC_036; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Untreated Control GSM5743899 RC_007_baseline_IFX_NR_RNA Peripheral Whole-Blood Patient: RC_007; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: Baseline; Diagnosis: CD Treatment control marker detected.
Unassigned Unassigned GSM5743712 13_2w_IFX_R_RNA Peripheral Whole-Blood Patient: 13; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 2w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743714 13_6w_IFX_R_RNA Peripheral Whole-Blood Patient: 13; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 6w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743716 13_14w_IFX_R_RNA Peripheral Whole-Blood Patient: 13; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 14w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743721 14_6w_IFX_R_RNA Peripheral Whole-Blood Patient: 14; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 6w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743722 14_14w_IFX_R_RNA Peripheral Whole-Blood Patient: 14; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 14w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743736 38_2w_IFX_NR_RNA Peripheral Whole-Blood Patient: 38; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 2w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743737 38_6w_IFX_NR_RNA Peripheral Whole-Blood Patient: 38; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 6w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743739 38_14w_IFX_NR_RNA Peripheral Whole-Blood Patient: 38; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 14w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743744 13_4h_IFX_R_RNA Peripheral Whole-Blood Patient: 13; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 4h; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743747 13_24h_IFX_R_RNA Peripheral Whole-Blood Patient: 13; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 24h; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743751 13_72h_IFX_R_RNA Peripheral Whole-Blood Patient: 13; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 72h; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743755 14_4h_IFX_R_RNA Peripheral Whole-Blood Patient: 14; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 4h; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743758 40_2w_IFX_R_RNA Peripheral Whole-Blood Patient: 40; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 2w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743759 14_24h_IFX_R_RNA Peripheral Whole-Blood Patient: 14; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 24h; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743761 40_14w_IFX_R_RNA Peripheral Whole-Blood Patient: 40; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 14w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743768 14_2w_IFX_R_RNA Peripheral Whole-Blood Patient: 14; Cohort: Discovery - Infliximab; Treatment: Infliximab; Remission at week 14: Remission; Time point: 2w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743771 3_2w_VDZ_NR_RNA Peripheral Whole-Blood Patient: 3; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Non-remission; Time point: 2w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743773 3_6w_VDZ_NR_RNA Peripheral Whole-Blood Patient: 3; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Non-remission; Time point: 6w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743775 3_14w_VDZ_NR_RNA Peripheral Whole-Blood Patient: 3; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Non-remission; Time point: 14w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743776 7_2w_VDZ_R_RNA Peripheral Whole-Blood Patient: 7; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Remission; Time point: 2w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743778 7_6w_VDZ_R_RNA Peripheral Whole-Blood Patient: 7; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Remission; Time point: 6w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743780 7_14w_VDZ_R_RNA Peripheral Whole-Blood Patient: 7; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Remission; Time point: 14w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743791 41_24h_VDZ_NR_RNA Peripheral Whole-Blood Patient: 41; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Non-remission; Time point: 24h; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743794 25_2w_VDZ_R_RNA Peripheral Whole-Blood Patient: 25; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Remission; Time point: 2w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743796 25_6w_VDZ_R_RNA Peripheral Whole-Blood Patient: 25; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Remission; Time point: 6w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743798 25_14w_VDZ_R_RNA Peripheral Whole-Blood Patient: 25; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Remission; Time point: 14w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743805 26_4h_VDZ_NR_RNA Peripheral Whole-Blood Patient: 26; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Non-remission; Time point: 4h; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743806 19_2w_VDZ_NR_RNA Peripheral Whole-Blood Patient: 19; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Non-remission; Time point: 2w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743807 26_24h_VDZ_NR_RNA Peripheral Whole-Blood Patient: 26; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Non-remission; Time point: 24h; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743809 19_6w_VDZ_NR_RNA Peripheral Whole-Blood Patient: 19; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Non-remission; Time point: 6w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743810 19_14w_VDZ_NR_RNA Peripheral Whole-Blood Patient: 19; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Non-remission; Time point: 14w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743811 26_2w_VDZ_NR_RNA Peripheral Whole-Blood Patient: 26; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Non-remission; Time point: 2w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743815 26_6w_VDZ_NR_RNA Peripheral Whole-Blood Patient: 26; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Non-remission; Time point: 6w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743817 25_4h_VDZ_R_RNA Peripheral Whole-Blood Patient: 25; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Remission; Time point: 4h; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743819 26_14w_VDZ_NR_RNA Peripheral Whole-Blood Patient: 26; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Non-remission; Time point: 14w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743822 25_24h_VDZ_R_RNA Peripheral Whole-Blood Patient: 25; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Remission; Time point: 24h; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743823 41_4h_VDZ_NR_RNA Peripheral Whole-Blood Patient: 41; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Non-remission; Time point: 4h; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743832 31_2w_VDZ_R_RNA Peripheral Whole-Blood Patient: 31; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Remission; Time point: 2w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743834 31_6w_VDZ_R_RNA Peripheral Whole-Blood Patient: 31; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Remission; Time point: 6w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743835 31_14w_VDZ_R_RNA Peripheral Whole-Blood Patient: 31; Cohort: Discovery - Vedolizumab; Treatment: Vedolizumab; Remission at week 14: Remission; Time point: 14w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743842 RC_144_6w_IFX_R_RNA Peripheral Whole-Blood Patient: RC_144; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Remission; Time point: 6w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743843 RC_022_2w_IFX_R_RNA Peripheral Whole-Blood Patient: RC_022; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Remission; Time point: 2w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743844 RC_010_6w_IFX_NR_RNA Peripheral Whole-Blood Patient: RC_010; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 6w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743847 RC_116_2w_IFX_R_RNA Peripheral Whole-Blood Patient: RC_116; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Remission; Time point: 2w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743849 RC_116_6w_IFX_R_RNA Peripheral Whole-Blood Patient: RC_116; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Remission; Time point: 6w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743852 RC_004_6w_IFX_NR_RNA Peripheral Whole-Blood Patient: RC_004; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Non-remission; Time point: 6w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743853 RC_012_6w_IFX_R_RNA Peripheral Whole-Blood Patient: RC_012; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Remission; Time point: 6w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743854 RC_142_6w_IFX_R_RNA Peripheral Whole-Blood Patient: RC_142; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Remission; Time point: 6w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743862 RC_140_6w_IFX_R_RNA Peripheral Whole-Blood Patient: RC_140; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Remission; Time point: 6w; Diagnosis: CD No explicit case or control marker detected.
Unassigned Unassigned GSM5743864 RC_036_2w_IFX_R_RNA Peripheral Whole-Blood Patient: RC_036; Cohort: Replication; Treatment: Infliximab; Remission at week 14: Remission; Time point: 2w; Diagnosis: CD No explicit case or control marker detected.
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External Validation Finder

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