Identification and validation of aryl hydrocarbon receptor-associated hub genes in ulcerative colitis via integrated bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41094572", "kind": "science-record", "revision": 3, "content_hash": "sha256:16c70f60b940f2c15c9fc416f8eeba11811677553ecf9aaf14b770bf1b151ede", "created_at": "2026-11-01T20:31:09Z", "updated_at": "2026-11-01T22:14:50Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and validation of aryl hydrocarbon receptor-associated hub genes in ulcerative colitis via integrated bioinformatics analysis.", "doi": "10.1186/s40246-025-00835-5", "pmid": "41094572", "authors": ["Yuanpei Zhao", "Jiaping Wang", "Xiaoli Min", "Fuqiong Jiang", "Kaiwen Shi", "Hongyuan Liu", "Yichen Hu", "Wenliang Li", "Weiming Li"], "journal": "Human genomics", "year": 2025, "abstract": "OBJECTIVE: Ulcerative colitis (UC), a chronic inflammatory bowel disease, continues to pose substantial challenges in both diagnosis and treatment. The aryl hydrocarbon receptor (AhR) plays a pivotal role in intestinal immune regulation; however, its core regulatory network in the progression of UC remains largely undefined. This study aims to identify core UC-related genes associated with AhR and to validate their expression in dextran sulfate sodium (DSS)-induced murine models, thereby elucidating potential mechanisms underlying UC progression.\nMETHODS: Using the GSE75214 and GSE87466 datasets from the Gene Expression Omnibus (GEO) database, immune cell infiltration was quantified via the CIBERSORT algorithm. Candidate genes were identified through differential expression analysis, weighted gene co-expression network analysis (WGCNA) module selection, and construction of an AhR co-expression network. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) were performed, followed by construction of a protein-protein interaction (PPI) network using STRING and application of two machine learning algorithms to identify AhR-associated hub genes. Finally, the expression of key genes was validated in DSS-induced UC mouse models using real-time quantitative real-time quantitative polymerase chain reaction (RT-qPCR).\nRESULTS: A total of nine AHR-related shared genes were identified, which were significantly enriched in immune response, amino acid metabolism, and oxidative stress pathways. Through integration of the PPI network and machine learning approaches, three central hub genes (PPARG, IL1B, and IDO1) were identified. Immune infiltration analysis revealed pronounced immune dysregulation during the progression of UC, which may contribute to disease development. Animal experiments confirmed the expression of these three key genes in colonic tissues, and hematoxylin-eosin (H&E) staining revealed extensive infiltration of inflammatory cells, consistent with the bioinformatics findings.\nCONCLUSION: PPARG, IL1B, and IDO1 were identified as potential key genes closely associated with AHR, suggesting their possible involvement in modulating AhR signaling in UC, thereby offering a theoretical basis for disease diagnosis and therapeutic strategies.", "claims": [{"id": "claim-method", "statement": "ROC curve analysis demonstrated that all three hub genes achieved AUC values exceeding 0.8, indicating strong diagnostic performance for UC (GSE75214: PPARG, AUC = 0.984; IL1B, AUC = 0.954; IDO1, AUC = 0.942; GSE87466: PPARG, AUC = 0.924; IL1B, AUC = 0.968; IDO1, AUC = 0.953) (Fig. 6D).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41094572", "locator": "sections[19] \"Identification of hub genes via machine learning algorithms\" paragraph 2", "quote": "ROC curve analysis demonstrated that all three hub genes achieved AUC values exceeding 0.8, indicating strong diagnostic performance for UC (GSE75214: PPARG, AUC = 0.984; IL1B, AUC = 0.954; IDO1, AUC = 0.942; GSE87466: PPARG, AUC = 0.924; IL1B, AUC = 0.968; IDO1, AUC = 0.953) (Fig. 6D)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed during the current study are available in the Gene Expression Omnibus (GEO). The data used in this study can be accessed at the following links: GSE75214([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214)), GSE87466([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87466)), GSE38713([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38713)), GSE47908([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47908)), GSE([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53306)), and GSE37283([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37283)). The data that support the findings of this study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41094572", "locator": "sections[31] \"notes\" paragraph 1", "quote": "The datasets analyzed during the current study are available in the Gene Expression Omnibus (GEO). The data used in this study can be accessed at the following links: GSE75214([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214)), GSE87466([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87466)), GSE38713([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38713)), GSE47908([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47908)), GSE([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53306)), and GSE37283([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37283)). The data that support the findings of this study are available from the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "PPARG, IL1B, and IDO1 were identified as potential key genes closely associated with AHR, suggesting their possible involvement in modulating AhR signaling in UC, thereby offering a theoretical basis for disease diagnosis and therapeutic strategies.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41094572", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "PPARG, IL1B, and IDO1 were identified as potential key genes closely associated with AHR, suggesting their possible involvement in modulating AhR signaling in UC, thereby offering a theoretical basis for disease diagnosis and therapeutic strategies."}, {"asset": "source:pmid:41094572", "locator": "sections[19] \"Identification of hub genes via machine learning algorithms\" paragraph 2", "quote": "ROC curve analysis demonstrated that all three hub genes achieved AUC values exceeding 0.8, indicating strong diagnostic performance for UC (GSE75214: PPARG, AUC = 0.984; IL1B, AUC = 0.954; IDO1, AUC = 0.942; GSE87466: PPARG, AUC = 0.924; IL1B, AUC = 0.968; IDO1, AUC = 0.953) (Fig. 6D)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "PPARG, IL1B, and IDO1 were identified as potential key genes closely associated with AHR, suggesting their possible involvement in modulating AhR signaling in UC, thereby offering a theoretical basis for disease diagnosis and therapeutic strategies.", "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:41094572"], "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:GSE37283"], "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:GSE37283"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41094572", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s40246-025-00835-5", "sha256": "sha256:d0214efcee1409a96ec3fe23c1ebcdcdb4ffc0ac4b7f2df72891d3da558ed76a", "bytes": 55124, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s40246-025-00835-5", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12522315", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE37283", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37283", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE37283", "version": null, "note": "The datasets analyzed during the current study are available in the Gene Expression Omnibus (GEO). The data used in this study can be accessed at the following links: GSE75214([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214)), GSE87466([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87466)), GSE38713([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38713)), GSE47908([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47908)), GSE([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53306)), and GSE37283([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37283)). The data that support the findings of this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the current study are available in the Gene Expression Omnibus (GEO). The data used in this study can be accessed at the following links: GSE75214([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214)), GSE87466([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87466)), GSE38713([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38713)), GSE47908([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47908)), GSE([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53306)), and GSE37283([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37283)). The data that support the findings of this study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM915451", "GSM915452", "GSM915453", "GSM915454", "GSM915455", "GSM915456", "GSM915457", "GSM915458", "GSM915459", "GSM915460", "GSM915461", "GSM915462", "GSM915463", "GSM915464", "GSM915465", "GSM915466", "GSM915467", "GSM915468", "GSM915469", "GSM915470"], "sample_count": 20, "group_sizes": null, "group_sizes_basis": null, "platform": "13158", "taxon": "Homo sapiens", "title": "Gene Expression Changes in Non-Dysplastic Mucosa from Patients with Ulcerative Colitis Harboring Remote Neoplastic Lesions", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE38713", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38713", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE38713", "version": null, "note": "The datasets analyzed during the current study are available in the Gene Expression Omnibus (GEO). The data used in this study can be accessed at the following links: GSE75214([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214)), GSE87466([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87466)), GSE38713([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38713)), GSE47908([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47908)), GSE([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53306)), and GSE37283([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37283)). The data that support the findings of this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the current study are available in the Gene Expression Omnibus (GEO). The data used in this study can be accessed at the following links: GSE75214([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214)), GSE87466([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87466)), GSE38713([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38713)), GSE47908([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47908)), GSE([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53306)), and GSE37283([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37283)). The data that support the findings of this study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM948550", "GSM948551", "GSM948552", "GSM948553", "GSM948554", "GSM948555", "GSM948556", "GSM948557", "GSM948558", "GSM948559", "GSM948560", "GSM948561", "GSM948562", "GSM948563", "GSM948564", "GSM948565", "GSM948566", "GSM948567", "GSM948568", "GSM948569", "GSM948570", "GSM948571", "GSM948572", "GSM948573", "GSM948574", "GSM948575", "GSM948576", "GSM948577", "GSM948578", "GSM948579", "GSM948580", "GSM948581", "GSM948582", "GSM948583", "GSM948584", "GSM948585", "GSM948586", "GSM948587", "GSM948588", "GSM948589", "GSM948590", "GSM948591", "GSM948592"], "sample_count": 43, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from intestinal mucosa of patients with UC", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE47908", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47908", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE47908", "version": null, "note": "The datasets analyzed during the current study are available in the Gene Expression Omnibus (GEO). The data used in this study can be accessed at the following links: GSE75214([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214)), GSE87466([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87466)), GSE38713([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38713)), GSE47908([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47908)), GSE([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53306)), and GSE37283([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37283)). The data that support the findings of this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the current study are available in the Gene Expression Omnibus (GEO). The data used in this study can be accessed at the following links: GSE75214([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214)), GSE87466([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87466)), GSE38713([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38713)), GSE47908([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47908)), GSE([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53306)), and GSE37283([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37283)). 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The data used in this study can be accessed at the following links: GSE75214([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214)), GSE87466([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87466)), GSE38713([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38713)), GSE47908([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47908)), GSE([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53306)), and GSE37283([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37283)). The data that support the findings of this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the current study are available in the Gene Expression Omnibus (GEO). The data used in this study can be accessed at the following links: GSE75214([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214)), GSE87466([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87466)), GSE38713([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38713)), GSE47908([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47908)), GSE([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53306)), and GSE37283([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37283)). The data that support the findings of this study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1289168", "GSM1289169", "GSM1289170", "GSM1289171", "GSM1289172", "GSM1289173", "GSM1289174", "GSM1289175", "GSM1289176", "GSM1289177", "GSM1289178", "GSM1289179", "GSM1289180", "GSM1289181", "GSM1289182", "GSM1289183", "GSM1289184", "GSM1289185", "GSM1289186", "GSM1289187", "GSM1289188", "GSM1289189", "GSM1289190", "GSM1289191", "GSM1289192", "GSM1289193", "GSM1289194", "GSM1289195", "GSM1289196", "GSM1289197", "GSM1289198", "GSM1289199", "GSM1289200", "GSM1289201", "GSM1289202", "GSM1289203", "GSM1289204", "GSM1289205", "GSM1289206", "GSM1289207"], "sample_count": 40, "group_sizes": null, "group_sizes_basis": null, "platform": "14951", "taxon": "Homo sapiens", "title": "Differential Gene Expression between Active and Quiescent Stages of Ulcerative Colitis: Insights into a Distinctive Pathogenesis Profile", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE75214", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE75214", "version": null, "note": "The datasets analyzed during the current study are available in the Gene Expression Omnibus (GEO). The data used in this study can be accessed at the following links: GSE75214([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214)), GSE87466([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87466)), GSE38713([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38713)), GSE47908([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47908)), GSE([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53306)), and GSE37283([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37283)). The data that support the findings of this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the current study are available in the Gene Expression Omnibus (GEO). The data used in this study can be accessed at the following links: GSE75214([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214)), GSE87466([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87466)), GSE38713([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38713)), GSE47908([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47908)), GSE([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53306)), and GSE37283([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37283)). The data that support the findings of this study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1426071", "GSM1426072", "GSM1426073", "GSM1426074", "GSM1426075", "GSM1426076", "GSM1426077", "GSM1426078", "GSM1426079", "GSM1426080", "GSM1426081", "GSM1426082", "GSM1426083", "GSM1426084", "GSM1426085", "GSM1426086", "GSM1426087", "GSM1426088", "GSM1426089", "GSM1426090", "GSM1426091", "GSM1426092", "GSM1426093", "GSM1426094", "GSM1426095", "GSM1426096", "GSM1426097", "GSM1426098", "GSM1426099", "GSM1426100", "GSM1426101", "GSM1426102", "GSM1426103", "GSM1426104", "GSM1426105", "GSM1426106", "GSM1426107", "GSM1426108", "GSM1426109", "GSM1426110", "GSM1426111", "GSM1426112", "GSM1426113", "GSM1426114", "GSM1426115", "GSM1426116", "GSM1426117", "GSM1426118", "GSM1426119", "GSM1426120", "GSM1426121", "GSM1426122", "GSM1426123", "GSM1426124", "GSM1426125", "GSM1426126", "GSM1426127", "GSM1426128", "GSM1426129", "GSM1426130", "GSM1426131", "GSM1426132", "GSM1426133", "GSM1426134", "GSM1426135", "GSM1426136", "GSM1426137", "GSM1426138", "GSM1426139", "GSM1426140", "GSM1426141", "GSM1426142", "GSM1426143", "GSM1426144", "GSM1426145", "GSM1426146", "GSM1426147", "GSM1426148", "GSM1426149", "GSM1426150", "GSM1426151", "GSM1426152", "GSM1426153", "GSM1426154", "GSM1426155", "GSM1426156", "GSM1426157", "GSM1426158", "GSM1426159", "GSM1426160", "GSM1426161", "GSM1426162", "GSM1426163", "GSM1426164", "GSM1426165", "GSM1426166", "GSM1426167", "GSM1426168", "GSM1426169", "GSM1426170", "GSM1426171", "GSM1426172", "GSM1426173", "GSM1426174", "GSM1426175", "GSM1426176", "GSM1426177", "GSM1426178", "GSM1426179", "GSM1426180", "GSM1426181", "GSM1426182", "GSM1426183", "GSM1426184", "GSM1426185", "GSM1426186", "GSM1945759", "GSM1945760", "GSM1945761", "GSM1945762", "GSM1945763", "GSM1945764", "GSM1945765", "GSM1945766", "GSM1945767", "GSM1945768", "GSM1945769", "GSM1945770", "GSM1945771", "GSM1945772", "GSM1945773", "GSM1945774", "GSM1945775", "GSM1945776", "GSM1945777", "GSM1945778", "GSM1945779", "GSM1945780", "GSM1945781", "GSM1945782", "GSM1945783", "GSM1945784", "GSM1945785", "GSM1945786", "GSM1945787", "GSM1945788", "GSM1945789", "GSM1945790", "GSM1945791", "GSM1945792", "GSM1945793", "GSM1945794", "GSM1945795", "GSM1945796", "GSM1945797", "GSM1945798", "GSM1945799", "GSM1945800", "GSM1945801", "GSM1945802", "GSM1945803", "GSM1945804", "GSM1945805", "GSM1945806", "GSM1945807", "GSM1945808", "GSM1945809", "GSM1945810", "GSM1945811", "GSM1945812", "GSM1945813", "GSM1945814", "GSM1945815", "GSM1945816", "GSM1945817", "GSM1945818", "GSM1945819", "GSM1945820", "GSM1945821", "GSM1945822", "GSM1945823", "GSM1945824", "GSM1945825", "GSM1945826", "GSM1945827", "GSM1945828", "GSM1945829", "GSM1945830", "GSM1945831", "GSM1945832", "GSM1945833", "GSM1945834", "GSM1945835", "GSM1945836"], "sample_count": 194, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Mucosal gene expression profiling in patients with inflammatory bowel disease study", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE87466", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87466", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE87466", "version": null, "note": "The datasets analyzed during the current study are available in the Gene Expression Omnibus (GEO). The data used in this study can be accessed at the following links: GSE75214([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214)), GSE87466([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87466)), GSE38713([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38713)), GSE47908([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47908)), GSE([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53306)), and GSE37283([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37283)). The data that support the findings of this study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed during the current study are available in the Gene Expression Omnibus (GEO). The data used in this study can be accessed at the following links: GSE75214([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214)), GSE87466([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87466)), GSE38713([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38713)), GSE47908([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47908)), GSE([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53306)), and GSE37283([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37283)). The data that support the findings of this study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2332098", "GSM2332099", "GSM2332100", "GSM2332101", "GSM2332102", "GSM2332103", "GSM2332104", "GSM2332105", "GSM2332106", "GSM2332107", "GSM2332108", "GSM2332109", "GSM2332110", "GSM2332111", "GSM2332112", "GSM2332113", "GSM2332114", "GSM2332115", "GSM2332116", "GSM2332117", "GSM2332118", "GSM2332119", "GSM2332120", "GSM2332121", "GSM2332122", "GSM2332123", "GSM2332124", "GSM2332125", "GSM2332126", "GSM2332127", "GSM2332128", "GSM2332129", "GSM2332130", "GSM2332131", "GSM2332132", "GSM2332133", "GSM2332134", "GSM2332135", "GSM2332136", "GSM2332137", "GSM2332138", "GSM2332139", "GSM2332140", "GSM2332141", "GSM2332142", "GSM2332143", "GSM2332144", "GSM2332145", "GSM2332146", "GSM2332147", "GSM2332148", "GSM2332149", "GSM2332150", "GSM2332151", "GSM2332152", "GSM2332153", "GSM2332154", "GSM2332155", "GSM2332156", "GSM2332157", "GSM2332158", "GSM2332159", "GSM2332160", "GSM2332161", "GSM2332162", "GSM2332163", "GSM2332164", "GSM2332165", "GSM2332166", "GSM2332167", "GSM2332168", "GSM2332169", "GSM2332170", "GSM2332171", "GSM2332172", "GSM2332173", "GSM2332174", "GSM2332175", "GSM2332176", "GSM2332177", "GSM2332178", "GSM2332179", "GSM2332180", "GSM2332181", "GSM2332182", "GSM2332183", "GSM2332184", "GSM2332185", "GSM2332186", "GSM2332187", "GSM2332188", "GSM2332189", "GSM2332190", "GSM2332191", "GSM2332192", "GSM2332193", "GSM2332194", "GSM2332195", "GSM2332196", "GSM2332197", "GSM2332198", "GSM2332199", "GSM2332200", "GSM2332201", "GSM2332202", "GSM2332203", "GSM2332204", "GSM2332205"], "sample_count": 108, "group_sizes": null, "group_sizes_basis": null, "platform": "13158", "taxon": "Homo sapiens", "title": "Gene expression profiling of mucosal biopsies from adult patients with moderately to severely active ulcerative colitis", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE37283 not downloaded", "asset:data:geo:GSE37283 licence not read", "asset:data:geo:GSE38713 not downloaded", "asset:data:geo:GSE38713 licence not read", "asset:data:geo:GSE47908 not downloaded", "asset:data:geo:GSE47908 licence not read", "asset:data:geo:GSE53306 not downloaded", "asset:data:geo:GSE53306 licence not read", "asset:data:geo:GSE75214 not downloaded", "asset:data:geo:GSE75214 licence not read", "asset:data:geo:GSE87466 not downloaded", "asset:data:geo:GSE87466 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": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.8, "band": "high", "quote": "ROC curve"}}, {"id": "method-3", "family": null, "specific": null, "label": "Receiver operating characteristic (ROC) curve analysis with area under the curve (AUC)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "ROC curve analysis demonstrated that all three hub genes achieved AUC values exceeding 0.8, indicating strong diagnostic performance for UC (GSE75214: PPARG, AUC = 0.984; IL1B, AUC = 0.954; IDO1, AUC = 0.942; GSE87466: PPARG, AUC = 0.924; IL1B, AUC = 0.968; IDO1, AUC = 0.953) (Fig. 6D)."}}], "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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE75214", "GSE87466", "GSE38713", "GSE47908", "GSE53306", "GSE37283"], "resolved_accessions": ["GSE75214", "GSE87466", "GSE38713", "GSE47908", "GSE53306", "GSE37283"], "statements": ["The datasets analyzed during the current study are available in the Gene Expression Omnibus (GEO). The data used in this study can be accessed at the following links: GSE75214([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214)), GSE87466([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87466)), GSE38713([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38713)), GSE47908([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47908)), GSE([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53306)), and GSE37283([GEO Accession viewer](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37283)). The data that support the findings of this study are available from the corresponding author upon reasonable request."], "basis": "The paper names GSE75214, GSE87466, GSE38713, GSE47908, GSE53306, GSE37283 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:41094572", "data:geo:GSE37283"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE37283"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:03:15Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13588, "completion_tokens": 2434, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:41094572", "type": "paper", "label": "pmid:41094572"}, {"id": "source:pmid:41094572", "type": "manuscript", "label": "PMID 41094572 full text"}, {"id": "data:geo:GSE37283", "type": "dataset", "label": "GEO GSE37283"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41094572", "type": "paper", "label": "pmid:41094572"}, {"id": "source:pmid:41094572", "type": "manuscript", "label": "PMID 41094572 full text"}, {"id": "data:geo:GSE37283", "type": "dataset", "label": "GEO GSE37283"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41094572", "type": "extraction", "used": ["source:pmid:41094572"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE37283", "type": "accession_resolution", "used": ["data:geo:GSE37283"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:41094572", "parent_hash": "sha256:79cc21fbb6cc499cd8fd9e03c64f2f9d48c3fe8f3158dac44ac844a0101523ce", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE37283 licence not read", "asset:data:geo:GSE37283 not downloaded", "asset:data:geo:GSE38713 licence not read", "asset:data:geo:GSE38713 not downloaded", "asset:data:geo:GSE47908 licence not read", "asset:data:geo:GSE47908 not downloaded", "asset:data:geo:GSE53306 licence not read", "asset:data:geo:GSE53306 not downloaded", "asset:data:geo:GSE75214 licence not read", "asset:data:geo:GSE75214 not downloaded", "asset:data:geo:GSE87466 licence not read", "asset:data:geo:GSE87466 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["sion in dextran sulfate sodium (DSS)-induced murine models, thereby elucidating potential mechan", "of key genes was validated in DSS-induced UC mouse models using real-time quantitative real-tim"], "order_basis": "paper_text_order:567", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["time quantitative polymerase chain reaction (RT-qPCR). RESULTS: A total of nine AHR-related share", "e quantitative polymerase chain reaction (RT-qPCR). RESULTS: A total of nine AHR-related share"], "order_basis": "paper_text_order:1472", "id": "assay:2"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}