Prognostic implications of metabolism-associated gene signatures in colorectal cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32953273", "kind": "science-record", "revision": 8, "content_hash": "sha256:3fec510a013d268fb7d86138d44789229a0a9e6881d7fecb62da0318c7bc0fa1", "created_at": "2026-11-01T15:41:10Z", "updated_at": "2026-11-01T22:45:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prognostic implications of metabolism-associated gene signatures in colorectal cancer.", "doi": "10.7717/peerj.9847", "pmid": "32953273", "authors": ["Yandong Miao", "Qiutian Li", "Jiangtao Wang", "Wuxia Quan", "Chen Li", "Yuan Yang", "Denghai Mi"], "journal": "PeerJ", "year": 2020, "abstract": "Colorectal cancer (CRC) is one of the most common and deadly malignancies. Novel biomarkers for the diagnosis and prognosis of this disease must be identified. Besides, metabolism plays an essential role in the occurrence and development of CRC. This article aims to identify some critical prognosis-related metabolic genes (PRMGs) and construct a prognosis model of CRC patients for clinical use. We obtained the expression profiles of CRC from The Cancer Genome Atlas database (TCGA), then identified differentially expressed PRMGs by R and Perl software. Hub genes were filtered out by univariate Cox analysis and least absolute shrinkage and selection operator Cox analysis. We used functional enrichment analysis methods, such as Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Gene Set Enrichment Analysis, to identify involved signaling pathways of PRMGs. The nomogram predicted overall survival (OS). Calibration traces were used to evaluate the consistency between the actual and the predicted survival rate. Finally, a prognostic model was constructed based on six metabolic genes (NAT2, XDH, GPX3, AKR1C4, SPHK1, and ADCY5), and the risk score was an independent prognostic prognosticator. Genetic expression and risk score were significantly correlated with clinicopathologic characteristics of CRC. A nomogram based on the clinicopathological feature of CRC and risk score accurately predicted the OS of individual CRC cancer patients. We also validated the results in the independent colorectal cancer cohorts GSE39582 and GSE87211. Our study demonstrates that the risk score is an independent prognostic biomarker and is closely correlated with the malignant clinicopathological characteristics of CRC patients. We also determined some metabolic genes associated with the survival and clinical stage of CRC as potential biomarkers for CRC diagnosis and treatment.", "claims": [{"id": "claim-method", "statement": "We screened differentially expressed metabolism-related genes using the Wilcox Test with R-package “edgeR” (Robinson, McCarthy & Smyth, 2010), and “limma”.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32953273", "locator": "sections[4] \"Identification of prognosis-associated metabolism-related genes\" paragraph 2", "quote": "We screened differentially expressed metabolism-related genes using the Wilcox Test with R-package “edgeR” (Robinson, McCarthy & Smyth, 2010), and “limma”."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:The data are available at NCBI GEO (GSE39582, GSE87211) and at TCGA.The search instructions for TCGA:(1) Case keywords: “colon, rectosigmoid junction, and rectum [Primary Site]”, “TCGA[Program]”, “TCGA-COAD, TCGA-READ [Project]”, “Adenomas and Adenocarcinomas [Disease Type]”.(2) File keywords: “Transcriptome Profiling [Data Category]”, “Gene Expression Quantification [Data Category]”, “RNA-Seq [Experimental Strategy]”, “HTSeq—FPKM [Workflow Type]”, “Clinical [Data Category]”, “BCR XML [Data Format]”.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32953273", "locator": "sections[18] \"Additional Information and Declarations\" paragraph 4", "quote": "The following information was supplied regarding data availability:The data are available at NCBI GEO (GSE39582, GSE87211) and at TCGA.The search instructions for TCGA:(1) Case keywords: “colon, rectosigmoid junction, and rectum [Primary Site]”, “TCGA[Program]”, “TCGA-COAD, TCGA-READ [Project]”, “Adenomas and Adenocarcinomas [Disease Type]”.(2) File keywords: “Transcriptome Profiling [Data Category]”, “Gene Expression Quantification [Data Category]”, “RNA-Seq [Experimental Strategy]”, “HTSeq—FPKM [Workflow Type]”, “Clinical [Data Category]”, “BCR XML [Data Format]”."}], "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:32953273"], "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:GSE39582"], "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:GSE39582"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32953273", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.9847", "sha256": "sha256:95f06c803b9fc7c8b4b10ad1997d231fab83d5686adf6bf968dc3c07c0e452e3", "bytes": 39035, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.9847", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7474523", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE39582", "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=GSE39582", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE39582", "version": null, "note": "The following information was supplied regarding data availability:The data are available at NCBI GEO (GSE39582, GSE87211) and at TCGA.The search instructions for TCGA:(1) Case keywords: “colon, rectosigmoid junction, and rectum [Primary Site]”, “TCGA[Program]”, “TCGA-COAD, TCGA-READ [Project]”, “Adenomas and Adenocarcinomas [Disease Type]”.(2) File keywords: “Transcriptome Profiling [Data Category]”, “Gene Expression Quantification [Data Category]”, “RNA-Seq [Experimental Strategy]”, “HTSeq—FPKM [Workflow Type]”, “Clinical [Data Category]”, “BCR XML [Data Format]”.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:The data are available at NCBI GEO (GSE39582, GSE87211) and at TCGA.The search instructions for TCGA:(1) Case keywords: “colon, rectosigmoid junction, and rectum [Primary Site]”, “TCGA[Program]”, “TCGA-COAD, TCGA-READ [Project]”, “Adenomas and Adenocarcinomas [Disease Type]”.(2) File keywords: “Transcriptome Profiling [Data Category]”, “Gene Expression Quantification [Data Category]”, “RNA-Seq [Experimental Strategy]”, “HTSeq—FPKM [Workflow Type]”, “Clinical [Data Category]”, “BCR XML [Data Format]”.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1681353", "GSM1681354", "GSM1681355", "GSM1681356", "GSM1681357", "GSM1681358", "GSM1681359", "GSM1681360", "GSM1681361", "GSM1681362", "GSM1681363", "GSM1681364", "GSM1681365", "GSM1681366", "GSM1681367", "GSM1681368", "GSM1681369", "GSM1681370", "GSM1681371", "GSM971957", "GSM971958", "GSM971959", "GSM971960", "GSM971961", "GSM971962", "GSM971963", "GSM971964", "GSM971965", "GSM971966", "GSM971967", "GSM971968", "GSM971969", "GSM971970", "GSM971971", "GSM971972", "GSM971973", "GSM971974", "GSM971975", "GSM971976", "GSM971977", "GSM971978", "GSM971979", "GSM971980", "GSM971981", "GSM971982", "GSM971983", "GSM971984", "GSM971985", "GSM971986", "GSM971987", "GSM971988", "GSM971989", "GSM971990", "GSM971991", "GSM971992", "GSM971993", "GSM971994", "GSM971995", "GSM971996", "GSM971997", "GSM971998", "GSM971999", "GSM972000", "GSM972001", "GSM972002", "GSM972003", "GSM972004", "GSM972005", "GSM972006", "GSM972007", "GSM972008", "GSM972009", "GSM972010", "GSM972011", "GSM972012", "GSM972013", "GSM972014", "GSM972015", "GSM972016", "GSM972017", "GSM972018", "GSM972019", "GSM972020", "GSM972021", "GSM972022", "GSM972023", "GSM972024", "GSM972025", "GSM972026", "GSM972027", "GSM972028", "GSM972029", "GSM972030", "GSM972031", "GSM972032", "GSM972033", "GSM972034", "GSM972035", "GSM972036", "GSM972037", "GSM972038", "GSM972039", "GSM972040", "GSM972041", "GSM972042", "GSM972043", "GSM972044", "GSM972045", "GSM972046", "GSM972047", "GSM972048", "GSM972049", "GSM972050", "GSM972051", "GSM972052", "GSM972053", "GSM972054", "GSM972055", "GSM972056", "GSM972057", "GSM972058", "GSM972059", "GSM972060", "GSM972061", "GSM972062", "GSM972063", "GSM972064", "GSM972065", "GSM972066", "GSM972067", "GSM972068", "GSM972069", "GSM972070", "GSM972071", "GSM972072", "GSM972073", "GSM972074", "GSM972075", "GSM972076", "GSM972077", "GSM972078", "GSM972079", "GSM972080", "GSM972081", "GSM972082", "GSM972083", "GSM972084", "GSM972085", "GSM972086", "GSM972087", "GSM972088", "GSM972089", "GSM972090", "GSM972091", "GSM972092", "GSM972093", "GSM972094", "GSM972095", "GSM972096", "GSM972097", "GSM972098", "GSM972099", "GSM972100", "GSM972101", "GSM972102", "GSM972103", "GSM972104", "GSM972105", "GSM972106", "GSM972107", "GSM972108", "GSM972109", "GSM972110", "GSM972111", "GSM972112", "GSM972113", "GSM972114", "GSM972115", "GSM972116", "GSM972117", "GSM972118", "GSM972119", "GSM972120", "GSM972121", "GSM972122", "GSM972123", "GSM972124", "GSM972125", "GSM972126", "GSM972127", "GSM972128", "GSM972129", "GSM972130", "GSM972131", "GSM972132", "GSM972133", "GSM972134", "GSM972135", "GSM972136", "GSM972137", "GSM972138", "GSM972139", "GSM972140", "GSM972141", "GSM972142", "GSM972143", "GSM972144", "GSM972145", "GSM972146", "GSM972147", "GSM972148", "GSM972149", "GSM972150", "GSM972151", "GSM972152", "GSM972153", "GSM972154", "GSM972155", "GSM972156", "GSM972157", "GSM972158", "GSM972159", "GSM972160", "GSM972161", "GSM972162", "GSM972163", "GSM972164", "GSM972165", "GSM972166", "GSM972167", "GSM972168", "GSM972169", "GSM972170", "GSM972171", "GSM972172", "GSM972173", "GSM972174", "GSM972175", "GSM972176", "GSM972177", "GSM972178", "GSM972179", "GSM972180", "GSM972181", "GSM972182", "GSM972183", "GSM972184", "GSM972185", "GSM972186", "GSM972187", "GSM972188", "GSM972189", "GSM972190", "GSM972191", "GSM972192", "GSM972193", "GSM972194", "GSM972195", "GSM972196", "GSM972197", "GSM972198", "GSM972199", "GSM972200", "GSM972201", "GSM972202", "GSM972203", "GSM972204", "GSM972205", "GSM972206", "GSM972207", "GSM972208", "GSM972209", "GSM972210", "GSM972211", "GSM972212", "GSM972213", "GSM972214", "GSM972215", "GSM972216", "GSM972217", "GSM972218", "GSM972219", "GSM972220", "GSM972221", "GSM972222", "GSM972223", "GSM972224", "GSM972225", "GSM972226", "GSM972227", "GSM972228", "GSM972229", "GSM972230", "GSM972231", "GSM972232", "GSM972233", "GSM972234", "GSM972235", "GSM972236", "GSM972237", "GSM972238", "GSM972239", "GSM972240", "GSM972241", "GSM972242", "GSM972243", "GSM972244", "GSM972245", "GSM972246", "GSM972247", "GSM972248", "GSM972249", "GSM972250", "GSM972251", "GSM972252", "GSM972253", "GSM972254", "GSM972255", "GSM972256", "GSM972257", "GSM972258", "GSM972259", "GSM972260", "GSM972261", "GSM972262", "GSM972263", "GSM972264", "GSM972265", "GSM972266", "GSM972267", "GSM972268", "GSM972269", "GSM972270", "GSM972271", "GSM972272", "GSM972273", "GSM972274", "GSM972275", "GSM972276", "GSM972277", "GSM972278", "GSM972279", "GSM972280", "GSM972281", "GSM972282", "GSM972283", "GSM972284", "GSM972285", "GSM972286", "GSM972287", "GSM972288", "GSM972289", "GSM972290", "GSM972291", "GSM972292", "GSM972293", "GSM972294", "GSM972295", "GSM972296", "GSM972297", "GSM972298", "GSM972299", "GSM972300", "GSM972301", "GSM972302", "GSM972303", "GSM972304", "GSM972305", "GSM972306", "GSM972307", "GSM972308", "GSM972309", "GSM972310", "GSM972311", "GSM972312", "GSM972313", "GSM972314", "GSM972315", "GSM972316", "GSM972317", "GSM972318", "GSM972319", "GSM972320", "GSM972321", "GSM972322", "GSM972323", "GSM972324", "GSM972325", "GSM972326", "GSM972327", "GSM972328", "GSM972329", "GSM972330", "GSM972331", "GSM972332", "GSM972333", "GSM972334", "GSM972335", "GSM972336", "GSM972337", "GSM972338", "GSM972339", "GSM972340", "GSM972341", "GSM972342", "GSM972343", "GSM972344", "GSM972345", "GSM972346", "GSM972347", "GSM972348", "GSM972349", "GSM972350", "GSM972351", "GSM972352", "GSM972353", "GSM972354", "GSM972355", "GSM972356", "GSM972357", "GSM972358", "GSM972359", "GSM972360", "GSM972361", "GSM972362", "GSM972363", "GSM972364", "GSM972365", "GSM972366", "GSM972367", "GSM972368", "GSM972369", "GSM972370", "GSM972371", "GSM972372", "GSM972373", "GSM972374", "GSM972375", "GSM972376", "GSM972377", "GSM972378", "GSM972379", "GSM972380", "GSM972381", "GSM972382", "GSM972383", "GSM972384", "GSM972385", "GSM972386", "GSM972387", "GSM972388", "GSM972389", "GSM972390", "GSM972391", "GSM972392", "GSM972393", "GSM972394", "GSM972395", "GSM972396", "GSM972397", "GSM972398", "GSM972399", "GSM972400", "GSM972401", "GSM972402", "GSM972403", "GSM972404", "GSM972405", "GSM972406", "GSM972407", "GSM972408", "GSM972409", "GSM972410", "GSM972411", "GSM972412", "GSM972413", "GSM972414", "GSM972415", "GSM972416", "GSM972417", "GSM972418", "GSM972419", "GSM972420", "GSM972421", "GSM972422", "GSM972423", "GSM972424", "GSM972425", "GSM972426", "GSM972427", "GSM972428", "GSM972429", "GSM972430", "GSM972431", "GSM972432", "GSM972433", "GSM972434", "GSM972435", "GSM972436", "GSM972437", "GSM972438", "GSM972439", "GSM972440", "GSM972441", "GSM972442", "GSM972443", "GSM972444", "GSM972445", "GSM972446", "GSM972447", "GSM972448", "GSM972449", "GSM972450", "GSM972451", "GSM972452", "GSM972453", "GSM972454", "GSM972455", "GSM972456", "GSM972457", "GSM972458", "GSM972459", "GSM972460", "GSM972461", "GSM972462", "GSM972463", "GSM972464", "GSM972465", "GSM972466", "GSM972467", "GSM972468", "GSM972469", "GSM972470", "GSM972471", "GSM972472", "GSM972473", "GSM972474", "GSM972475", "GSM972476", "GSM972477", "GSM972478", "GSM972479", "GSM972480", "GSM972481", "GSM972482", "GSM972483", "GSM972484", "GSM972485", "GSM972486", "GSM972487", "GSM972488", "GSM972489", "GSM972490", "GSM972491", "GSM972492", "GSM972493", "GSM972494", "GSM972495", "GSM972496", "GSM972497", "GSM972498", "GSM972499", "GSM972500", "GSM972501", "GSM972502", "GSM972503", "GSM972504", "GSM972505", "GSM972506", "GSM972507", "GSM972508", "GSM972509", "GSM972510", "GSM972511", "GSM972512", "GSM972513", "GSM972514", "GSM972515", "GSM972516", "GSM972517", "GSM972518", "GSM972519", "GSM972520", "GSM972521", "GSM972522"], "sample_count": 585, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics [Expression]", "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:GSE87211", "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=GSE87211", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE87211", "version": null, "note": "The following information was supplied regarding data availability:The data are available at NCBI GEO (GSE39582, GSE87211) and at TCGA.The search instructions for TCGA:(1) Case keywords: “colon, rectosigmoid junction, and rectum [Primary Site]”, “TCGA[Program]”, “TCGA-COAD, TCGA-READ [Project]”, “Adenomas and Adenocarcinomas [Disease Type]”.(2) File keywords: “Transcriptome Profiling [Data Category]”, “Gene Expression Quantification [Data Category]”, “RNA-Seq [Experimental Strategy]”, “HTSeq—FPKM [Workflow Type]”, “Clinical [Data Category]”, “BCR XML [Data Format]”.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:The data are available at NCBI GEO (GSE39582, GSE87211) and at TCGA.The search instructions for TCGA:(1) Case keywords: “colon, rectosigmoid junction, and rectum [Primary Site]”, “TCGA[Program]”, “TCGA-COAD, TCGA-READ [Project]”, “Adenomas and Adenocarcinomas [Disease Type]”.(2) File keywords: “Transcriptome Profiling [Data Category]”, “Gene Expression Quantification [Data Category]”, “RNA-Seq [Experimental Strategy]”, “HTSeq—FPKM [Workflow Type]”, “Clinical [Data Category]”, “BCR XML [Data Format]”.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2325238", "GSM2325239", "GSM2325240", "GSM2325241", "GSM2325242", "GSM2325243", "GSM2325244", "GSM2325245", "GSM2325246", "GSM2325247", "GSM2325248", "GSM2325249", "GSM2325250", "GSM2325251", "GSM2325252", "GSM2325253", "GSM2325254", "GSM2325255", "GSM2325256", "GSM2325257", "GSM2325258", "GSM2325259", "GSM2325260", "GSM2325261", "GSM2325262", "GSM2325263", "GSM2325264", "GSM2325265", "GSM2325266", "GSM2325267", "GSM2325268", "GSM2325269", "GSM2325270", "GSM2325271", "GSM2325272", "GSM2325273", "GSM2325274", "GSM2325275", "GSM2325276", "GSM2325277", "GSM2325278", "GSM2325279", "GSM2325280", "GSM2325281", "GSM2325282", "GSM2325283", "GSM2325284", "GSM2325285", "GSM2325286", "GSM2325287", "GSM2325288", "GSM2325289", "GSM2325290", "GSM2325291", "GSM2325292", "GSM2325293", "GSM2325294", "GSM2325295", "GSM2325296", "GSM2325297", "GSM2325298", "GSM2325299", "GSM2325300", "GSM2325301", "GSM2325302", "GSM2325303", "GSM2325304", "GSM2325305", "GSM2325306", "GSM2325307", "GSM2325308", "GSM2325309", "GSM2325310", "GSM2325311", "GSM2325312", "GSM2325313", "GSM2325314", "GSM2325315", "GSM2325316", "GSM2325317", "GSM2325318", "GSM2325319", "GSM2325320", "GSM2325321", "GSM2325322", "GSM2325323", "GSM2325324", "GSM2325325", "GSM2325326", "GSM2325327", "GSM2325328", "GSM2325329", "GSM2325330", "GSM2325331", "GSM2325332", "GSM2325333", "GSM2325334", "GSM2325335", "GSM2325336", "GSM2325337", "GSM2325338", "GSM2325339", "GSM2325340", "GSM2325341", "GSM2325342", "GSM2325343", "GSM2325344", "GSM2325345", "GSM2325346", "GSM2325347", "GSM2325348", "GSM2325349", "GSM2325350", "GSM2325351", "GSM2325352", "GSM2325353", "GSM2325354", "GSM2325355", "GSM2325356", "GSM2325357", "GSM2325358", "GSM2325359", "GSM2325360", "GSM2325361", "GSM2325362", "GSM2325363", "GSM2325364", "GSM2325365", "GSM2325366", "GSM2325367", "GSM2325368", "GSM2325369", "GSM2325370", "GSM2325371", "GSM2325372", "GSM2325373", "GSM2325374", "GSM2325375", "GSM2325376", "GSM2325377", "GSM2325378", "GSM2325379", "GSM2325380", "GSM2325381", "GSM2325382", "GSM2325383", "GSM2325384", "GSM2325385", "GSM2325386", "GSM2325387", "GSM2325388", "GSM2325389", "GSM2325390", "GSM2325391", "GSM2325392", "GSM2325393", "GSM2325394", "GSM2325395", "GSM2325396", "GSM2325397", "GSM2325398", "GSM2325399", "GSM2325400", "GSM2325401", "GSM2325402", "GSM2325403", "GSM2325404", "GSM2325405", "GSM2325406", "GSM2325407", "GSM2325408", "GSM2325409", "GSM2325410", "GSM2325411", "GSM2325412", "GSM2325413", "GSM2325414", "GSM2325415", "GSM2325416", "GSM2325417", "GSM2325418", "GSM2325419", "GSM2325420", "GSM2325421", "GSM2325422", "GSM2325423", "GSM2325424", "GSM2325425", "GSM2325426", "GSM2325427", "GSM2325428", "GSM2325429", "GSM2325430", "GSM2325431", "GSM2325432", "GSM2325433", "GSM2325434", "GSM2325435", "GSM2325436", "GSM2325437", "GSM2325438", "GSM2325439", "GSM2325440", "GSM2325441", "GSM2325442", "GSM2325443", "GSM2325444", "GSM2325445", "GSM2325446", "GSM2325447", "GSM2325448", "GSM2325449", "GSM2325450", "GSM2325451", "GSM2325452", "GSM2325453", "GSM2325454", "GSM2325455", "GSM2325456", "GSM2325457", "GSM2325458", "GSM2325459", "GSM2325460", "GSM2325461", "GSM2325462", "GSM2325463", "GSM2325464", "GSM2325465", "GSM2325466", "GSM2325467", "GSM2325468", "GSM2325469", "GSM2325470", "GSM2325471", "GSM2325472", "GSM2325473", "GSM2325474", "GSM2325475", "GSM2325476", "GSM2325477", "GSM2325478", "GSM2325479", "GSM2325480", "GSM2325481", "GSM2325482", "GSM2325483", "GSM2325484", "GSM2325485", "GSM2325486", "GSM2325487", "GSM2325488", "GSM2325489", "GSM2325490", "GSM2325491", "GSM2325492", "GSM2325493", "GSM2325494", "GSM2325495", "GSM2325496", "GSM2325497", "GSM2325498", "GSM2325499", "GSM2325500", "GSM2325501", "GSM2325502", "GSM2325503", "GSM2325504", "GSM2325505", "GSM2325506", "GSM2325507", "GSM2325508", "GSM2325509", "GSM2325510", "GSM2325511", "GSM2325512", "GSM2325513", "GSM2325514", "GSM2325515", "GSM2325516", "GSM2325517", "GSM2325518", "GSM2325519", "GSM2325520", "GSM2325521", "GSM2325522", "GSM2325523", "GSM2325524", "GSM2325525", "GSM2325526", "GSM2325527", "GSM2325528", "GSM2325529", "GSM2325530", "GSM2325531", "GSM2325532", "GSM2325533", "GSM2325534", "GSM2325535", "GSM2325536", "GSM2325537", "GSM2325538", "GSM2325539", "GSM2325540", "GSM2325541", "GSM2325542", "GSM2325543", "GSM2325544", "GSM2325545", "GSM2325546", "GSM2325547", "GSM2325548", "GSM2325549", "GSM2325550", "GSM2325551", "GSM2325552", "GSM2325553", "GSM2325554", "GSM2325555", "GSM2325556", "GSM2325557", "GSM2325558", "GSM2325559", "GSM2325560", "GSM2325561", "GSM2325562", "GSM2325563", "GSM2325564", "GSM2325565", "GSM2325566", "GSM2325567", "GSM2325568", "GSM2325569", "GSM2325570", "GSM2325571", "GSM2325572", "GSM2325573", "GSM2325574", "GSM2325575", "GSM2325576", "GSM2325577", "GSM2325578", "GSM2325579", "GSM2325580", "GSM2325581", "GSM2325582", "GSM2325583", "GSM2325584", "GSM2325585", "GSM2325586", "GSM2325587", "GSM2325588", "GSM2325589", "GSM2325590", "GSM2325591", "GSM2325592", "GSM2325593", "GSM2325594", "GSM2325595", "GSM2325596", "GSM2325597", "GSM2325598", "GSM2325599", "GSM2325600"], "sample_count": 363, "group_sizes": null, "group_sizes_basis": null, "platform": "13497", "taxon": "Homo sapiens", "title": "Colorectal cancer susceptibility loci as predictive markers of rectal cancer prognosis after surgery", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32953273:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:734f3146a06520dbf43bd74b24c4db898ee0b370ed8abe7fc8d639ec78702142", "bytes": 206, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#table-1", "version": null, "note": "Functions of genes in the prognostic gene signatures.", "structure": {"pmcid": "PMC7474523", "section_index": 10, "section_title": "Construction prognosis model for TCGA colorectal cancer cohort", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "Functions of genes in the prognostic gene signatures.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[10]/table-wrap[1]#table-1"}}], "gaps": ["asset:data:geo:GSE39582 not downloaded", "asset:data:geo:GSE39582 licence not read", "asset:data:geo:GSE87211 not downloaded", "asset:data:geo:GSE87211 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": "We screened differentially expressed metabolism-related genes using the Wilcox Test with R-package “edgeR” (Robinson, McCarthy & Smyth, 2010), 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": 0.8, "band": "high", "quote": "limma"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "pathway enrichment"}}], "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": ["GSE39582", "GSE87211"], "resolved_accessions": ["GSE39582", "GSE87211"], "statements": ["The following information was supplied regarding data availability:The data are available at NCBI GEO (GSE39582, GSE87211) and at TCGA.The search instructions for TCGA:(1) Case keywords: “colon, rectosigmoid junction, and rectum [Primary Site]”, “TCGA[Program]”, “TCGA-COAD, TCGA-READ [Project]”, “Adenomas and Adenocarcinomas [Disease Type]”.(2) File keywords: “Transcriptome Profiling [Data Category]”, “Gene Expression Quantification [Data Category]”, “RNA-Seq [Experimental Strategy]”, “HTSeq—FPKM [Workflow Type]”, “Clinical [Data Category]”, “BCR XML [Data Format]”."], "basis": "The paper names GSE39582, GSE87211 in NCBI 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:32953273", "data:geo:GSE39582", "asset:table:pmid:32953273:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE39582"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:22:39Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 29582, "completion_tokens": 2623, "cached_tokens": 776}}, "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:32953273", "type": "paper", "label": "pmid:32953273"}, {"id": "source:pmid:32953273", "type": "manuscript", "label": "PMID 32953273 full text"}, {"id": "data:geo:GSE39582", "type": "dataset", "label": "GEO GSE39582"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32953273", "type": "paper", "label": "pmid:32953273"}, {"id": "source:pmid:32953273", "type": "manuscript", "label": "PMID 32953273 full text"}, {"id": "data:geo:GSE39582", "type": "dataset", "label": "GEO GSE39582"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32953273", "type": "extraction", "used": ["source:pmid:32953273"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE39582", "type": "accession_resolution", "used": ["data:geo:GSE39582"], "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:32953273", "parent_hash": "sha256:9bbeca1fba775df542dd2584e8d6c9ad489e9ec6ec0c3fea2df9bf1a4f12e081", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE39582 licence not read", "asset:data:geo:GSE39582 not downloaded", "asset:data:geo:GSE87211 licence not read", "asset:data:geo:GSE87211 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": ["We screened differentially expressed metabolism-related genes using the Wilcox Test with R-package “edgeR” (Robinson, McCarthy & Smyth, 2010), and “limma”."], "order_basis": "analysis_only", "id": "assay:1"}]}