Identification of Differential Intestinal Mucosa Transcriptomic Biomarkers for Ulcerative Colitis by Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33144895", "kind": "science-record", "revision": 7, "content_hash": "sha256:c76170c1bf318052560d9f18fad1942e8354fe7d7d037a072c1ab5346ec38678", "created_at": "2026-11-01T15:41:14Z", "updated_at": "2026-11-01T22:02:27Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Differential Intestinal Mucosa Transcriptomic Biomarkers for Ulcerative Colitis by Bioinformatics Analysis.", "doi": "10.1155/2020/8876565", "pmid": "33144895", "authors": ["Fang Cheng", "Qiang Li", "Jinglin Wang", "Fang Zeng", "Kaiping Wang", "Yu Zhang"], "journal": "Disease markers", "year": 2020, "abstract": "BACKGROUND: Ulcerative colitis (UC) is a complicated disease caused by the interaction between genetic and environmental factors that affect mucosal homeostasis and triggers inappropriate immune response. The purpose of the study was to identify significant biomarkers with potential therapeutic targets and the underlying mechanisms.\nMETHODS: The gene expression profiles of GSE48958, GSE73661, and GSE59071 are from the GEO database. Differentially expressed genes (DEGs) were screened by the GEO2R tool. Next, the Database for Annotation, Visualization and Integrated Discovery (DAVID) was applied to analyze gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Then, protein-protein interaction (PPI) was visualized by Cytoscape with Search Tool for the Retrieval of Interacting Genes (STRING).\nRESULTS: There were a total of 128 common DEGs genes, including 86 upregulated genes enriched in extracellular space, regulation of inflammatory response, chemokine-mediated signaling pathway, response to lipopolysaccharide, and cell proliferation, while 42 downregulated genes enriched in the integral component of the membrane, the integral component of the plasma membrane, apical plasma membrane, symporter activity, and chloride channel activity. The KEGG pathway analysis results demonstrated that DEGs were particularly enriched in cytokine-cytokine receptor interaction, TNF signaling pathway, chemokine signaling pathway, pertussis, and rheumatoid arthritis. 18 central modules of the PPI networks were selected with Cytotype MCODE. Furthermore, 18 genes were found to significantly enrich in the extracellular space, inflammatory response, chemokine-mediated signaling pathway, TNF signaling pathway, regulation of cell proliferation, and immune response via reanalysis of DAVID.\nCONCLUSION: The study identified DEGs, key target genes, functional pathways, and pathway analysis of UC, which may provide potential molecular targets and diagnostic biomarkers for UC.", "claims": [{"id": "claim-method", "statement": "GEO2R was used for data preprocessing and applied to screen DEGs between the following groups: UC vs. control group.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33144895", "locator": "sections[4] \"2.2. 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This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE48958"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE48958"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33144895", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2020/8876565", "sha256": 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Module Analysis of the PPI Network", "row_count": 11, "column_count": 6}, "table": {"label": "Table 2", "caption": "Gene ontology analysis of 18 central hub genes in UC.", "rows": [["Category", "Term", "Count", "P value", "Genes", "--log10 (P value)"], ["GOTERM_BP_DIRECT", "GO:0070098~chemokine-mediated signaling pathway", "7", "8.79E-12", "CCL20, CXCL2, CXCR1, CXCL8, CXCL11, CXCL10", "7.977397"], ["GOTERM_BP_DIRECT", "GO:0006954~inflammatory response", "8", "3.40E-09", "CCL20, PTGS2, CXCL2, CXCL8, NOS2, CXCL11, CXCL10", "5.389683"], ["GOTERM_BP_DIRECT", "GO:0042127~regulation of cell proliferation", "7", "1.41E-08", "PTGS2, CXCL2, CXCL8, NOS2, CXCL11, CXCL10", "4.772917"], ["GOTERM_BP_DIRECT", "GO:0006955~immune response", "7", "1.42E-07", "CXCL2, IL1B, CXCL8, CXCL11, IL1A, CXCL10", "3.770405"], ["GOTERM_BP_DIRECT", "GO:0006935~chemotaxis", "5", "3.20E-07", "CCL20, CXCR1, CXCL11, CXCL10", "3.415649"], ["GOTERM_BP_DIRECT", "GO:0032496~response to lipopolysaccharide", "5", "2.71E-06", "CXCL2, CXCL8, CXCL11, CXCL10", "2.488617"], ["GOTERM_BP_DIRECT", "GO:0060326~cell chemotaxis", "4", "2.42E-05", "CCL20, CXCL2, CXCL10, ICAM1,", "1.537263"], ["GOTERM_CC_DIRECT", "GO:0005615~extracellular space", "13", "1.26E-11", "CCL20, MMP9, IL1RN, CXCL2, IL1B, CXCL8,CXCL11,SELE,IL1A, CXCL10, TIMP1", "7.981942"], ["GOTERM_MF_DIRECT", "GO:0008009~chemokine activity", "6", "7.11E-10", "CCL20, CXCL2, CXCL8, CXCL11, CXCL10", "6.189676"], ["GOTERM_MF_DIRECT", "GO:0045236~CXCR chemokine receptor binding", "4", "2.98E-07", "CXCL2, CXCL8, CXCL10", "3.567109"]], "row_count": 11, "column_count": 6, "numeric_cells": 51, "header_rows": 1, "locator": "section[12]/table-wrap[1]#tab2"}}], "gaps": ["asset:data:geo:GSE48958 not downloaded", "asset:data:geo:GSE48958 licence not read", "asset:data:geo:GSE59071 not downloaded", "asset:data:geo:GSE59071 licence not read", "asset:data:geo:GSE73661 not downloaded", "asset:data:geo:GSE73661 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-2", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "GO enrichment"}}, {"id": "method-3", "family": null, "specific": null, "label": "GEO2R differential expression analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "GEO2R was used for data preprocessing and applied to screen DEGs between the following groups: UC vs. control group."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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