Exploration of the core genes in ulcerative interstitial cystitis/bladder pain syndrome.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33848079", "kind": "science-record", "revision": 8, "content_hash": "sha256:60f9ca75d3c49772d36c8a6f4e495b12157c296a0978211b025268303d7a703f", "created_at": "2026-11-01T15:41:32Z", "updated_at": "2026-11-01T22:46:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploration of the core genes in ulcerative interstitial cystitis/bladder pain syndrome.", "doi": "10.1590/S1677-5538.IBJU.2020.1104", "pmid": "33848079", "authors": ["Hao Wu", "Quan-Xin Su", "Zi-Yi Zhang", "Ze Zhang", "Sheng-Lin Gao", "Chao Lu", "Li Zuo", "Li-Feng Zhang"], "journal": "International braz j urol : official journal of the Brazilian Society of Urology", "year": 2021, "abstract": "OBJECTIVE: Interstitial cystitis (IC)/bladder pain syndrome (BPS) is a chronic inflammatory disease that can cause bladder pain and accompanying symptoms, such as long-term urinary frequency and urgency. IC/BPS can be ulcerative or non-ulcerative. The aim of this study was to explore the core genes involved in the pathogenesis of ulcerative IC, and thus the potential biomarkers for clinical treatment.\nMATERIALS AND METHODS: First, the gene expression dataset GSE11783 was downloaded using the Gene Expression Omnibus (GEO) database and analyzed using the limma package in R to identify differentially expressed genes (DEGs). Then, the Database for Annotation, Visualization and Integrated Discovery (DAVID) was used for Gene Ontology (GO) functional analysis, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) was used for pathway enrichment analysis. Finally, the protein-protein interaction (PPI) network was constructed, and key modules and hub genes were determined using the STRING and Cytoscape software. The resulting key modules were then analyzed for tissue-specific gene expression using BioGPS.\nRESULTS: A total of 216 up-regulated DEGs and 267 down-regulated genes were identified, and three key modules and nine hub genes were obtained.\nCONCLUSION: The core genes (CXCL8, CXCL1, IL6) obtained in this study may be potential biomarkers of interstitial cystitis with guiding significance for clinical treatment.", "claims": [{"id": "claim-method", "statement": "the limma package was used to perform difference analysis, identify the DEGs between ulcerative IC group, non-ulcerative IC group and normal control group, and to calculate the adjusted P value and long FC.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33848079", "locator": "sections[4] \"Data Preprocessing and Identification of DEGs\" paragraph 2", "quote": "the limma package was used to perform difference analysis, identify the DEGs between ulcerative IC group, non-ulcerative IC group and normal control group, and to calculate the adjusted P value and long FC."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The authors confirm that the data supporting these research results is provided in this article and its supplementary materials.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33848079", "locator": "sections[19] \"Footnotes\" paragraph 2", "quote": "The authors confirm that the data supporting these research results is provided in this article and its supplementary materials."}], "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:33848079"], "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:GSE11783"], "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:GSE11783"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33848079", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1590/S1677-5538.IBJU.2020.1104", "sha256": 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materials.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The authors confirm that the data supporting these research results is provided in this article and its supplementary materials.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM298203", "GSM298204", "GSM298205", "GSM298206", "GSM298207", "GSM298208", "GSM298209", "GSM298210", "GSM298211", "GSM298212", "GSM298213", "GSM298214", "GSM298215", "GSM298216", "GSM298217", "GSM402541"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression profile of bladder tissue of patients with ulcerative interstitial cystitis", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33848079:1", "role": "table", "format": "jats-table", 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"sha256:7d40fa2284116872dc12798c547710827d5c6fc7050e6672d5078d436e9602ba", "bytes": 443, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#t2", "version": null, "note": "The Tissue-specific expressed genes identified by BioGPS.", "structure": {"pmcid": "PMC8321495", "section_index": 13, "section_title": "Tissue-specific expression analysis of key modules", "row_count": 6, "column_count": 2}, "table": {"label": "Table 2", "caption": "The Tissue-specific expressed genes identified by BioGPS.", "rows": [["System", "Genes"], ["Hematologic/immune", "CCL21, GPR18, C5AR1, PPBP, ICOS"], ["Neurologic", "SELE"], ["Skin/ muscle", "CXCL6, CXCL8, CXCL1, CXCL5, CCL11, MMP3, IL6, CCL8, MMP1"], ["Reproductive", "MMP10, GATA3"], ["Endocrine", "PPARG, TNFRSF11B"]], "row_count": 6, "column_count": 2, "numeric_cells": 4, "header_rows": 1, "locator": "section[13]/table-wrap[1]#t2"}}, {"id": "asset:table:pmid:33848079:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:34090a84ee8159fa242eefd5b135931ae0ce5eb885839ed05cedef89bdf062cd", "bytes": 719, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#t3", "version": null, "note": "The top 15 hub genes resulting from each ranking method.", "structure": {"pmcid": "PMC8321495", "section_index": 14, "section_title": "Identification of hub gene", "row_count": 16, "column_count": 4}, "table": {"label": "Table 3", "caption": "The top 15 hub genes resulting from each ranking method.", "rows": [["Closeness", "Degree", "EPC", "Radiality"], ["PECAM1", "PECAM1", "PECAM1", "PECAM1"], ["PTGS2", "PTGS2", "MMP9", "PTGS2"], ["MMP9", "MMP9", "PTGS2", "MMP9"], ["BMP2", "CXCL1", "CXCL1", "BMP2"], ["THY1", "CXCL8", "CXCL13", "THY1"], ["PPARG", "CD86", "CCL19", "PPARG"], ["CXCL1", "CXCL5", "CD86", "CXCL1"], ["CXCL8", "IL6", 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