Bioinformatics analysis-based mining of potential markers for inflammatory bowel disease and their immune relevance.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39262455", "kind": "science-record", "revision": 3, "content_hash": "sha256:2119f649683100408515c8ca3b3ad76f63ae78ee9103dd7588c6b00ee5f2d3b1", "created_at": "2026-11-01T20:29:24Z", "updated_at": "2026-11-01T22:12:39Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics analysis-based mining of potential markers for inflammatory bowel disease and their immune relevance.", "doi": "10.21037/tcr-24-274", "pmid": "39262455", "authors": ["Yuwen Zhu", "Yanbin Pan", "Lichao Fan", "Meng Zou", "Yingjie Liu", "Jiayi Hu", "Shijun Xia", "Yue Li", "Ruijie Dai", "Wenjiang Wu"], "journal": "Translational cancer research", "year": 2024, "abstract": "Background: The incidence of inflammatory bowel disease (IBD) is increasing every year and is characterized by a prolonged course, frequent relapses, difficulty in curing, and a lack of more efficacious therapeutic biomarkers. The aim of this study was to find key core genes as therapeutic biomarkers for IBD.\nMethods: GSE75214 in Gene Expression Omnibus (GEO) was used as the experimental set. The genes in the top 25% of standard deviation of all samples in the experimental set were subjected to systematic weighted gene co-expression network analysis (WGCNA) to find candidate genes. Then, least absolute shrinkage and selection operator (LASSO) logistic regression was used to further screen the central genes. Finally, the validity of hub genes was verified on GEO dataset GSE179285 using \"BiocManager\" R package.\nResults: Twelve well-preserved modules were identified in the experimental set using the WGCNA method. Among them, five modules significantly associated with IBD were screened as clinically significant modules, and four candidate genes were screened from these five modules. Then TIMP1, GUCA2B, and HIF1A were screened as hub genes. These hub genes successfully distinguished tumor samples from healthy tissues by artificial neural network algorithm in an independent test set with an area under the working characteristic curve of 0.946 for the subjects.\nConclusions: IBD differentially expressed gene (DEGs) are involved in immunoregulatory processes. TIMP1, GUCA2B, and HIF1A, as core genes of IBD, have the potential to be therapeutic targets for patients with IBD, and our findings may provide a new outlook on the future treatment of IBD.", "claims": [{"id": "claim-method", "statement": "The genes in the top 25% of standard deviation of all samples in the experimental set were subjected to systematic weighted gene co-expression network analysis (WGCNA) to find candidate genes. Then, least absolute shrinkage and selection operator (LASSO) logistic regression was used to further screen the central genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39262455", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The genes in the top 25% of standard deviation of all samples in the experimental set were subjected to systematic weighted gene co-expression network analysis (WGCNA) to find candidate genes. Then, least absolute shrinkage and selection operator (LASSO) logistic regression was used to further screen the central genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "GSE75214 (11) based on the GPL6244 platform [(HuGene-1_0-st) Affymetrix Human Gene 1.0 ST Array] included gene expression profiles of 172 cases of diseased colon tissues and 22 cases of normal colon tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39262455", "locator": "sections[4] \"Data collection\" paragraph 2", "quote": "GSE75214 (11) based on the GPL6244 platform [(HuGene-1_0-st) Affymetrix Human Gene 1.0 ST Array] included gene expression profiles of 172 cases of diseased colon tissues and 22 cases of normal colon tissues."}], "state": "complete"}, {"id": "claim-target-result", "statement": "TIMP1, GUCA2B, and HIF1A were screened as hub genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39262455", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Then TIMP1, GUCA2B, and HIF1A were screened as hub genes."}, {"asset": "source:pmid:39262455", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "These hub genes successfully distinguished tumor samples from healthy tissues by artificial neural network algorithm in an independent test set with an area under the working characteristic curve of 0.946 for the subjects."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "TIMP1, GUCA2B, and HIF1A were screened as hub genes.", "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:39262455"], "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:GSE179285"], "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:GSE179285"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39262455", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tcr-24-274", "sha256": 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