Bioinformatics Analysis of Differentially Expressed Genes and Protein-Protein Interaction Networks Associated with Functional Pathways in Ulcerative Colitis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33462173", "kind": "science-record", "revision": 9, "content_hash": "sha256:0f612fb2af91a05540a526ab4549ba4e36607d33676717ad83369b10e537d892", "created_at": "2026-11-01T15:41:23Z", "updated_at": "2026-11-01T22:46:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics Analysis of Differentially Expressed Genes and Protein-Protein Interaction Networks Associated with Functional Pathways in Ulcerative Colitis.", "doi": "10.12659/MSM.927917", "pmid": "33462173", "authors": ["Feng Cao", "Yun-Sheng Cheng", "Liang Yu", "Yan-Yan Xu", "Yong Wang"], "journal": "Medical science monitor : international medical journal of experimental and clinical research", "year": 2021, "abstract": "BACKGROUND This bioinformatics study aimed to identify differentially expressed genes (DEGs) and protein-protein interaction (PPI) networks associated with functional pathways in ulcerative colitis based on 3 Gene Expression Omnibus (GEO) datasets. MATERIAL AND METHODS The GSE87466, GSE75214, and GSE48958 MINiML formatted family files were downloaded from the GEO database. DEGs were identified from the 3 datasets, and volcano maps and heat maps were drawn after R language standardization and analysis, respectively. Venn diagram software was used to identify common DEGs. PPI analysis of common DEGs was performed using the Search Tool for the Retrieval of Interacting Genes. Gene modules and hub genes were visualized in the PPI network using Cytoscape. Enrichment analysis was performed for all common DEGs, module genes, and hub genes. RESULTS A total of 90 DEGs were selected, which included 3 functional modules and 1 hub gene module. CXCL8 module genes were mainly enriched in cytokine-mediated signaling pathways and interleukin (IL)-10 signaling. CCL20 module genes were mainly enriched in the IL-17 signaling pathway and cellular response to IL-1. Hub gene modules mainly involved IL-10, IL-4, and IL-13 signaling pathways. CXCL8, CXCL1, and IL-1ß were the top 3 hub genes and were mainly involved in IL-10 signaling. CONCLUSIONS Bioinformatics analysis using 3 GEO datasets identified CXCL8, CXCL1, and IL-1ß, which are involved in IL-10 signaling, as the top 3 hub genes in ulcerative colitis. The findings from this study remain to be validated, but they may contribute to the further understanding of the pathogenesis of ulcerative colitis.", "claims": [{"id": "claim-method", "statement": "We used |logFC| >1.5 and P<0.05 as standards to identify DEGs through the “limma” R software package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33462173", "locator": "sections[4] \"Data processing and screening of DEGs\" paragraph 2", "quote": "We used |logFC| >1.5 and P<0.05 as standards to identify DEGs through the “limma” R software package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The GSE87466, GSE75214, and GSE48958 datasets contained 21, 11, and 8 normal tissue samples and 87, 97, and 13 UC colon tissue samples, respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33462173", "locator": "sections[3] \"Dataset information\" paragraph 2", "quote": "The GSE87466, GSE75214, and GSE48958 datasets contained 21, 11, and 8 normal tissue samples and 87, 97, and 13 UC colon tissue samples, respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:33462173"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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": {"log2fc_threshold": "oftware package, using |logFC| > 1"}, "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:33462173", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12659/MSM.927917", 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protein-coupled receptor signaling pathway;GO: 0008285 negative regulation of cell proliferation", "GO: i0005576 extracellular region;GO: 0005615 extracellular space", "GO: 0005125 cytokine activity;GO: 0005153 interleukin-8 receptor binding;GO: 0005515 protein binding;GO: 0008009 chemokine activity"], ["CXCL1", "GO: 0006935 chemotaxis;GO: 0006952 defense response;GO: 0006954 inflammatory response;GO: 0006955 immune response;GO: 0007165 signal transduction;GO: 0007186 G protein-coupled receptor signaling pathway;GO: 0007399 nervous system development;GO: 0008285 negative regulation of cell proliferation;GO: 0019221 cytokine-mediated signaling pathway;GO: 0030036 actin cytoskeleton organization;", "GO: 0005576 extracellular region;GO: 0005615 extracellular space;GO: 0035580 specific granule lumen;GO: 1904724 tertiary granule lumen", "GO: 0005102 signaling receptor binding;GO: 0005125 cytokine activity;GO: 0008009 chemokine activity;GO: 0008047 enzyme activator activity;GO: 0008083 growth factor activity"], ["IL1B", "GO: 0000165 MAPK cascade;GO: 0000187 activation of MAPK activity;GO: 0001660 fever generation;GO: 0001934 positive regulation of protein phosphorylation;GO: 0002711 positive regulation of T cell mediated immunity;GO: 0006915 apoptotic process;GO: 0006954 inflammatory response;GO: 0006955 immune response;GO: 0007165 signal transduction;GO: 0007267 cell-cell signaling", "GO: 0005576 extracellular region;GO: 0005615 extracellular space;GO: 0005737 cytoplasm;GO: 0005764 lysosome;GO: 0005776 autophagosome; GO: 0005829 cytosol;GO: 0030141 secretory granule;GO: 0031410 cytoplasmic vesicle;GO: 0031982 vesicle", "GO: 0005125 cytokine activity;GO: 0005149 interleukin-1 receptor binding;GO: 0005178 integrin binding;GO: 0005515 protein binding;GO: 0019904 protein domain specific binding"]], "row_count": 4, "column_count": 4, "numeric_cells": 9, "header_rows": 1, "locator": "section[12]/table-wrap[1]#t1-medscimonit-27-e927917"}}, {"id": 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