SynthesisScientific reports2021
Meta-analysis of gene expression disease signatures in colonic biopsy tissue from patients with ulcerative colitis.
Synthesis in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
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Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it, 35 citations in OpenAlex.
- A shared tissue transcriptome signature and pathways in psoriasis and ulcerative colitis.Scientific reports · 2022Pooled it
- Metabolism and response to stress gene signatures reveal ulcerative colitis heterogeneity and identify patients with increased response to therapy.Journal of Crohn's & colitis · 2025Trial
- Short-term caloric restriction partially reprograms immune and microbial networks during acute DSS-induced colitis.Genes & nutrition · 2026Article
- Pharmacogenomic Pathways Underlying Variable Vedolizumab Response in Crohn's Disease Patients: A Rare-Variant Analysis.Biomedicines · 2026Article
- IL-15 Promotes Inflammatory Th17 Cells in the Intestine.Inflammatory bowel diseases · 2025Article
- DEFB4A/hBD2, a non-invasive serum biomarker for detection of ulcerative colitis.Scientific reports · 2025Article
- PIWIL2 downregulation in colon cancer promotes transposon activity and pro-tumorigenic phenotypes.Biology open · 2025Article
- Mineralocorticoid receptor activation contributes to intestinal fibrosis through neutrophil gelatinase-associated lipocalin in preclinical models.Nature communications · 2025Article
- A comprehensive transcriptome based meta-analysis to unveil the aggression nexus of oral squamous cell carcinoma.Biochemistry and biophysics reports · 2025Article
- CGRPβ suppresses the pathogenesis of ulcerative colitis via the immunoproteasome.Scientific reports · 2025Article
- Establishment of an ulcerative colitis model using colon organoids derived from human induced pluripotent stem cells.iScience · 2024Article
- Natural approaches for the management of ulcerative colitis: evidence of preclinical and clinical investigations.Natural products and bioprospecting · 2024Review
- Challenges in Defining a Reference Set of Differentially Expressed lncRNAs in Ulcerative Colitis by Meta-Analysis.Current issues in molecular biology · 2024Article
- Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis.Nature communications · 2024Article
- Proteomic Differences in Colonic Epithelial Cells in Ulcerative Colitis Have an Epigenetic Basis.Gastro hep advances · 2024Article
- Exploring potential biomarkers and therapeutic targets in inflammatory bowel disease: insights from a mega-analysis approach.Frontiers in immunology · 2024Article
- AutoCore: A network-based definition of the core module of human autoimmunity and autoinflammation.Science advances · 2023Article
- Identification of Specific Biomarkers and Pathways in the Treatment Response of Infliximab for Inflammatory Bowel Disease: In-Silico Analysis.Life (Basel, Switzerland) · 2023Article
- Distinct transcriptional signatures in purified circulating immune cells drive heterogeneity in disease location in IBD.BMJ open gastroenterology · 2023Article
- Identifying metabolic shifts in Crohn's disease using' omics-driven contextualized computational metabolic network models.Scientific reports · 2023Article
Corrections and comments
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Authors and funding
11 authors at 7 institutions in 4 countries.
Funding
Abstract
Publicly available ulcerative colitis (UC) gene expression datasets from observational studies and clinical trials include inherently heterogeneous disease characteristics and methodology. We used meta-analysis to identify a robust UC gene signature from inflamed biopsies. Eight gene expression datasets derived from biopsy tissue samples from noninflammatory bowel disease (IBD) controls and areas of active inflammation from patients with UC were publicly available. Expression- and meta-data were downloaded with GEOquery. Differentially expressed genes (DEG) in individual datasets were defined as those with fold change > 1.5 and a Benjamini-Hochberg adjusted P value < .05. Meta-analysis of all DEG used a random effects model. Reactome pathway enrichment analysis was conducted. Meta-analysis identified 946 up- and 543 down-regulated genes in patients with UC compared to non-IBD controls (1.2 and 1.7 times fewer up- and down-regulated genes than the median of the individual datasets). Top-ranked up- and down-regulated DEG were LCN2 and AQP8. Multiple immune-related pathways (e.g., 'Chemokine receptors bind chemokine' and 'Interleukin-10 signaling') were significantly up-regulated in UC, while 'Biological oxidations' and 'Fatty acid metabolism' were downregulated. A web-based data-mining tool with the meta-analysis results was made available ( https://premedibd.com/genes.html ). A UC inflamed biopsy disease gene signature was derived. This signature may be an unbiased reference for comparison and improve the efficiency of UC biomarker studies by increasing confidence for identification of disease-related genes and pathways.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.