The co-expression of Crohn's disease and colon cancer network was analyzed by bioinformatics-CXCL1 tumour microenvironment and prognosis-related gene CXCL1.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39402186", "kind": "science-record", "revision": 4, "content_hash": "sha256:275a86976ff7a190eda335a96b1e9b4eae364d197aeadee572d4ee056fe9b1c2", "created_at": "2026-11-01T20:29:38Z", "updated_at": "2026-11-01T22:55:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The co-expression of Crohn's disease and colon cancer network was analyzed by bioinformatics-CXCL1 tumour microenvironment and prognosis-related gene CXCL1.", "doi": "10.1007/s12672-024-01423-0", "pmid": "39402186", "authors": ["Zijuan Mao", "Yuyang Gu", "Ganxue Tao", "Qiang Dai", "Yangjie Xu", "Zhenghua Fei"], "journal": "Discover oncology", "year": 2024, "abstract": "PURPOSE: This study aimed to investigate the molecular links and mechanisms between Crohn's disease (CD) and colorectal cancer (CRC).\nMETHODS: This study used the Gene Expression Omnibus (GEO) database to identify Differentially expressed genes (DEGs) in CD (GSE112366) and CRC (GSE110224), analyzed by 'edgeR' and 'limma'. The Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes explored DEG functions, and the Search Tool for the Retrieval of Interacting Genes (STRING) informed the protein-protein interaction network construction visualized in Cytoscape (version 3.7.2). Cyto-Hubba identified key genes, whose biomarker potential for CD and CRC was evaluated.\nRESULTS: The study discovered 61 DEGs, with 44 up- and 17 down-regulated, linked to immune responses and signaling pathways. CXCL1, highly expressed in colon cancer, correlated with better prognosis and lower staging. It also showed associations with immune infiltration and checkpoint molecules, suggesting a role in cancer progression and retreat.\nCONCLUSION: CXCL1 may play a role in the development of colorectal cancer from inflammatory bowel disease.", "claims": [{"id": "claim-method", "statement": "This study used the Gene Expression Omnibus (GEO) database to identify Differentially expressed genes (DEGs) in CD (GSE112366) and CRC (GSE110224), analyzed by 'edgeR' and 'limma'.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39402186", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "This study used the Gene Expression Omnibus (GEO) database to identify Differentially expressed genes (DEGs) in CD (GSE112366) and CRC (GSE110224), analyzed by 'edgeR' and 'limma'."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. The data that support the results of the current study is available on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) websites.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39402186", "locator": "sections[16] \"Conclusion\" paragraph 3", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. The data that support the results of the current study is available on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) websites."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study discovered 61 DEGs, with 44 up- and 17 down-regulated, linked to immune responses and signaling pathways.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39402186", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The study discovered 61 DEGs, with 44 up- and 17 down-regulated, linked to immune responses and signaling pathways."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study discovered 61 DEGs, with 44 up- and 17 down-regulated, linked to immune responses and signaling pathways.", "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:39402186"], "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:GSE102133"], "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:GSE102133"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39402186", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s12672-024-01423-0", "sha256": "sha256:d6bcea2edc4d9dfb8979a1637e976a6ee4fdc74f97437c48510167b8be49f183", "bytes": 33307, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s12672-024-01423-0", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11479648", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE102133", "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=GSE102133", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE102133", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. The data that support the results of the current study is available on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) websites.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. The data that support the results of the current study is available on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) websites.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2728650", "GSM2728651", "GSM2728652", "GSM2728653", "GSM2728654", "GSM2728655", "GSM2728656", "GSM2728657", "GSM2728658", "GSM2728659", "GSM2728660", "GSM2728661", "GSM2728662", "GSM2728663", "GSM2728664", "GSM2728665", "GSM2728666", "GSM2728667", "GSM2728668", "GSM2728669", "GSM2728670", "GSM2728671", "GSM2728672", "GSM2728673", "GSM2728674", "GSM2728675", "GSM2728676", "GSM2728677", "GSM2728678", "GSM2728679", "GSM2728680", "GSM2728681", "GSM2728682", "GSM2728683", "GSM2728684", "GSM2728685", "GSM2728686", "GSM2728687", "GSM2728688", "GSM2728689", "GSM2728690", "GSM2728691", "GSM2728692", "GSM2728693", "GSM2728694", "GSM2728695", "GSM2728696", "GSM2728697", "GSM2728698", "GSM2728699", "GSM2728700", "GSM2728701", "GSM2728702", "GSM2728703", "GSM2728704", "GSM2728705", "GSM2728706", "GSM2728707", "GSM2728708", "GSM2728709", "GSM2728710", "GSM2728711", "GSM2728712", "GSM2728713", "GSM2728714", "GSM2728715", "GSM2728716", "GSM2728717", "GSM2728718", "GSM2728719", "GSM2728720", "GSM2728721", "GSM2728722", "GSM2728723", "GSM2728724", "GSM2728725", "GSM2728726"], "sample_count": 77, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Mucosal gene expression profiling in ileum of patients with Crohn's disease", "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:GSE110224", "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=GSE110224", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE110224", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. The data that support the results of the current study is available on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) websites.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. The data that support the results of the current study is available on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) websites.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2982932", "GSM2982933", "GSM2982934", "GSM2982935", "GSM2982936", "GSM2982937", "GSM2982938", "GSM2982939", "GSM2982940", "GSM2982941", "GSM2982942", "GSM2982943", "GSM2982944", "GSM2982945", "GSM2982946", "GSM2982947", "GSM2982948", "GSM2982949", "GSM2982950", "GSM2982951", "GSM2982952", "GSM2982953", "GSM2982954", "GSM2982955", "GSM2982956", "GSM2982957", "GSM2982958", "GSM2982959", "GSM2982960", "GSM2982961", "GSM2982962", "GSM2982963", "GSM2982964", "GSM2982965"], "sample_count": 34, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from 17 patients with colorectal cancer", "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:GSE112366", "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=GSE112366", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE112366", "version": null, "note": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. The data that support the results of the current study is available on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) websites.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. The data that support the results of the current study is available on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) websites.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3068409", "GSM3068410", "GSM3068411", "GSM3068412", "GSM3068413", "GSM3068414", "GSM3068415", "GSM3068416", "GSM3068417", "GSM3068418", "GSM3068419", "GSM3068420", "GSM3068421", "GSM3068422", "GSM3068423", "GSM3068424", "GSM3068425", "GSM3068426", "GSM3068427", "GSM3068428", "GSM3068429", "GSM3068430", "GSM3068431", "GSM3068432", "GSM3068433", "GSM3068434", "GSM3068435", "GSM3068436", "GSM3068437", "GSM3068438", "GSM3068439", "GSM3068440", "GSM3068441", "GSM3068442", "GSM3068443", "GSM3068444", "GSM3068445", "GSM3068446", "GSM3068447", "GSM3068448", "GSM3068449", "GSM3068450", "GSM3068451", "GSM3068452", "GSM3068453", "GSM3068454", "GSM3068455", "GSM3068456", "GSM3068457", "GSM3068458", "GSM3068459", "GSM3068460", "GSM3068461", "GSM3068462", "GSM3068463", "GSM3068464", "GSM3068465", "GSM3068466", "GSM3068467", "GSM3068468", "GSM3068469", "GSM3068470", "GSM3068471", "GSM3068472", "GSM3068473", "GSM3068474", "GSM3068475", "GSM3068476", "GSM3068477", "GSM3068478", "GSM3068479", "GSM3068480", "GSM3068481", "GSM3068482", "GSM3068483", "GSM3068484", "GSM3068485", "GSM3068486", "GSM3068487", "GSM3068488", "GSM3068489", "GSM3068490", "GSM3068491", "GSM3068492", "GSM3068493", "GSM3068494", "GSM3068495", "GSM3068496", "GSM3068497", "GSM3068498", "GSM3068499", "GSM3068500", "GSM3068501", "GSM3068502", "GSM3068503", "GSM3068504", "GSM3068505", "GSM3068506", "GSM3068507", "GSM3068508", "GSM3068509", "GSM3068510", "GSM3068511", "GSM3068512", "GSM3068513", "GSM3068514", "GSM3068515", "GSM3068516", "GSM3068517", "GSM3068518", "GSM3068519", "GSM3068520", "GSM3068521", "GSM3068522", "GSM3068523", "GSM3068524", "GSM3068525", "GSM3068526", "GSM3068527", "GSM3068528", "GSM3068529", "GSM3068530", "GSM3068531", "GSM3068532", "GSM3068533", "GSM3068534", "GSM3068535", "GSM3068536", "GSM3068537", "GSM3068538", "GSM3068539", "GSM3068540", "GSM3068541", "GSM3068542", "GSM3068543", "GSM3068544", "GSM3068545", "GSM3068546", "GSM3068547", "GSM3068548", "GSM3068549", "GSM3068550", "GSM3068551", "GSM3068552", "GSM3068553", "GSM3068554", "GSM3068555", "GSM3068556", "GSM3068557", "GSM3068558", "GSM3068559", "GSM3068560", "GSM3068561", "GSM3068562", "GSM3068563", "GSM3068564", "GSM3068565", "GSM3068566", "GSM3068567", "GSM3068568", "GSM3068569", "GSM3068570", "GSM3068571", "GSM3068572", "GSM3068573", "GSM3068574", "GSM3068575", "GSM3068576", "GSM3068577", "GSM3068578", "GSM3068579", "GSM3068580", "GSM3068581", "GSM3068582", "GSM3068583", "GSM3068584", "GSM3068585", "GSM3068586", "GSM3068587", "GSM3068588", "GSM3068589", "GSM3068590", "GSM3068591", "GSM3068592", "GSM3068593", "GSM3068594", "GSM3068595", "GSM3068596", "GSM3068597", "GSM3068598", "GSM3068599", "GSM3068600", "GSM3068601", "GSM3068602", "GSM3068603", "GSM3068604", "GSM3068605", "GSM3068606", "GSM3068607", "GSM3068608", "GSM3068609", "GSM3068610", "GSM3068611", "GSM3068612", "GSM3068613", "GSM3068614", "GSM3068615", "GSM3068616", "GSM3068617", "GSM3068618", "GSM3068619", "GSM3068620", "GSM3068621", "GSM3068622", "GSM3068623", "GSM3068624", "GSM3068625", "GSM3068626", "GSM3068627", "GSM3068628", "GSM3068629", "GSM3068630", "GSM3068631", "GSM3068632", "GSM3068633", "GSM3068634", "GSM3068635", "GSM3068636", "GSM3068637", "GSM3068638", "GSM3068639", "GSM3068640", "GSM3068641", "GSM3068642", "GSM3068643", "GSM3068644", "GSM3068645", "GSM3068646", "GSM3068647", "GSM3068648", "GSM3068649", "GSM3068650", "GSM3068651", "GSM3068652", "GSM3068653", "GSM3068654", "GSM3068655", "GSM3068656", "GSM3068657", "GSM3068658", "GSM3068659", "GSM3068660", "GSM3068661", "GSM3068662", "GSM3068663", "GSM3068664", "GSM3068665", "GSM3068666", "GSM3068667", "GSM3068668", "GSM3068669", "GSM3068670", "GSM3068671", "GSM3068672", "GSM3068673", "GSM3068674", "GSM3068675", "GSM3068676", "GSM3068677", "GSM3068678", "GSM3068679", "GSM3068680", "GSM3068681", "GSM3068682", "GSM3068683", "GSM3068684", "GSM3068685", "GSM3068686", "GSM3068687", "GSM3068688", "GSM3068689", "GSM3068690", "GSM3068691", "GSM3068692", "GSM3068693", "GSM3068694", "GSM3068695", "GSM3068696", "GSM3068697", "GSM3068698", "GSM3068699", "GSM3068700", "GSM3068701", "GSM3068702", "GSM3068703", "GSM3068704", "GSM3068705", "GSM3068706", "GSM3068707", "GSM3068708", "GSM3068709", "GSM3068710", "GSM3068711", "GSM3068712", "GSM3068713", "GSM3068714", "GSM3068715", "GSM3068716", "GSM3068717", "GSM3068718", "GSM3068719", "GSM3068720", "GSM3068721", "GSM3068722", "GSM3068723", "GSM3068724", "GSM3068725", "GSM3068726", "GSM3068727", "GSM3068728", "GSM3068729", "GSM3068730", "GSM3068731", "GSM3068732", "GSM3068733", "GSM3068734", "GSM3068735", "GSM3068736", "GSM3068737", "GSM3068738", "GSM3068739", "GSM3068740", "GSM3068741", "GSM3068742", "GSM3068743", "GSM3068744", "GSM3068745", "GSM3068746", "GSM3068747", "GSM3068748", "GSM3068749", "GSM3068750", "GSM3068751", "GSM3068752", "GSM3068753", "GSM3068754", "GSM3068755", "GSM3068756", "GSM3068757", "GSM3068758", "GSM3068759", "GSM3068760", "GSM3068761", "GSM3068762", "GSM3068763", "GSM3068764", "GSM3068765", "GSM3068766", "GSM3068767", "GSM3068768", "GSM3068769", "GSM3068770", "GSM3068771", "GSM3068772", "GSM3068773", "GSM3068774", "GSM3068775", "GSM3068776", "GSM3068777", "GSM3068778", "GSM3068779", "GSM3068780", "GSM3068781", "GSM3068782", "GSM3068783", "GSM3068784", "GSM3068785", "GSM3068786", "GSM3068787", "GSM3068788", "GSM3068789", "GSM3068790", "GSM3068791", "GSM3068792", "GSM3068793", "GSM3068794", "GSM3068795", "GSM3068796"], "sample_count": 388, "group_sizes": null, "group_sizes_basis": null, "platform": "13158", "taxon": "Homo sapiens", "title": "Intestinal epithelial microvilli are abnormal in Crohn's disease", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE102133 not downloaded", "asset:data:geo:GSE102133 licence not read", "asset:data:geo:GSE110224 not downloaded", "asset:data:geo:GSE110224 licence not read", "asset:data:geo:GSE112366 not downloaded", "asset:data:geo:GSE112366 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "edger", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "This study used the Gene Expression Omnibus (GEO) database to identify Differentially expressed genes (DEGs) in CD (GSE112366) and CRC (GSE110224), analyzed by 'edgeR' and 'limma'."}}, {"id": "method-2", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.7, "band": "medium", "quote": "limma"}}, {"id": "method-3", "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"}}], "targets": [], "gaps": []}, "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: edger."}, "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": ["GSE112366", "GSE110224", "GSE102133"], "resolved_accessions": ["GSE112366", "GSE110224", "GSE102133"], "statements": ["The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. The data that support the results of the current study is available on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) websites."], "basis": "The paper names GSE112366, GSE110224, GSE102133 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:39402186", "data:geo:GSE102133"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE102133"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:35:09Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9980, "completion_tokens": 1964, "cached_tokens": 0}}, "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:39402186", "type": "paper", "label": "pmid:39402186"}, {"id": "source:pmid:39402186", "type": "manuscript", "label": "PMID 39402186 full text"}, {"id": "data:geo:GSE102133", "type": "dataset", "label": "GEO GSE102133"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39402186", "type": "paper", "label": "pmid:39402186"}, {"id": "source:pmid:39402186", "type": "manuscript", "label": "PMID 39402186 full text"}, {"id": "data:geo:GSE102133", "type": "dataset", "label": "GEO GSE102133"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39402186", "type": "extraction", "used": ["source:pmid:39402186"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE102133", "type": "accession_resolution", "used": ["data:geo:GSE102133"], "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:39402186", "parent_hash": "sha256:a3aa82463b12acd7a0a1c2b07f919f4fd478cab05ac067ffdbcfcb583b902ba4", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE102133 licence not read", "asset:data:geo:GSE102133 not downloaded", "asset:data:geo:GSE110224 licence not read", "asset:data:geo:GSE110224 not downloaded", "asset:data:geo:GSE112366 licence not read", "asset:data:geo:GSE112366 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["This study used the Gene Expression Omnibus (GEO) database to identify Differentially expressed genes (DEGs) in CD (GSE112366) and CRC (GSE110224), analyzed by 'edgeR' and 'limma'."], "order_basis": "analysis_only", "id": "assay:1"}]}