Genes That Predict Poor Prognosis in Breast Cancer via Bioinformatical Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33959662", "kind": "science-record", "revision": 7, "content_hash": "sha256:e95ded8427d069d8309bd87d0719c105fb7f1c6f070209ad1e19f593151e7253", "created_at": "2026-11-01T15:41:34Z", "updated_at": "2026-11-01T22:03:42Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Genes That Predict Poor Prognosis in Breast Cancer via Bioinformatical Analysis.", "doi": "10.1155/2021/6649660", "pmid": "33959662", "authors": ["Qian Zhou", "Xiaofeng Liu", "Mingming Lv", "Erhu Sun", "Xun Lu", "Cheng Lu"], "journal": "BioMed research international", "year": 2021, "abstract": "BACKGROUND: Breast cancer is one of the most commonly diagnosed cancers all over the world, and it is now the leading cause of cancer death among females. The aim of this study was to find DEGs (differentially expressed genes) which can predict poor prognosis in breast cancer and be effective targets for breast cancer patients via bioinformatical analysis.\nMETHODS: GSE86374, GSE5364, and GSE70947 were chosen from the GEO database. DEGs between breast cancer tissues and normal breast tissues were picked out by GEO2R and Venn diagram software. Then, DAVID (Database for Annotation, Visualization, and Integrated Discovery) was used to analyze these DEGs in gene ontology (GO) including molecular function (MF), cellular component (CC), and biological process (BP) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway. Next, STRING (Search Tool for the Retrieval of Interacting Genes) was used to investigate potential protein-protein interaction (PPI) relationships among DEGs and these DEGs were analyzed by Molecular Complex Detection (MCODE) in Cytoscape. After that, UALCAN, GEPIA (gene expression profiling interactive analysis), and KM (Kaplan-Meier plotter) were used for the prognostic information and core genes were qualified.\nRESULTS: There were 96 upregulated genes and 98 downregulated genes in this study. 55 upregulated genes were selected as hub genes in the PPI network. For validation in UALCAN, GEPIA, and KM, 5 core genes (KIF4A, RACGAP1, CKS2, SHCBP1, and HMMR) were found to highly expressed in breast cancer tissues with poor prognosis. They differentially expressed between different subclasses of breast cancer.\nCONCLUSION: These five genes (KIF4A, RACGAP1, CKS2, SHCBP1, and HMMR) could be potential targets for therapy in breast cancer and prediction of prognosis on the basis of bioinformatical analysis.", "claims": [{"id": "claim-data-access", "statement": "The data used to support the findings of this study are available from the GEO database (https://www.ncbi.nlm.nih. gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33959662", "locator": "sections[19] \"Data Availability\" paragraph 2", "quote": "The data used to support the findings of this study are available from the GEO database (https://www.ncbi.nlm.nih. gov/geo/)."}], "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:33959662"], "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:GSE5364"], "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:GSE5364"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33959662", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2021/6649660", "sha256": "sha256:6b8ab975f8eebf49d13e9fb296956abbbabe614a37df4bc9ed63e5c327c61159", "bytes": 17109, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2021/6649660", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8075678", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE5364", "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=GSE5364", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE5364", "version": null, "note": "The data used to support the findings of this study are available from the GEO database (https://www.ncbi.nlm.nih. gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the GEO database (https://www.ncbi.nlm.nih. gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM121673", "GSM121674", "GSM121675", "GSM121676", "GSM121677", "GSM121678", "GSM121679", "GSM121680", "GSM121681", "GSM121682", "GSM121683", "GSM121684", "GSM121685", "GSM121686", "GSM121687", "GSM121688", "GSM121689", "GSM121690", "GSM121691", "GSM121692", "GSM121693", "GSM121694", "GSM121695", "GSM121696", "GSM121697", "GSM121698", "GSM121699", "GSM121700", "GSM121701", "GSM121702", "GSM121703", "GSM121704", "GSM121705", "GSM121706", "GSM121707", "GSM121708", "GSM121709", "GSM121710", "GSM121711", "GSM121712", "GSM121713", "GSM121714", "GSM121715", "GSM121716", "GSM121717", "GSM121718", "GSM121719", "GSM121720", "GSM121721", "GSM121722", "GSM121723", "GSM121724", "GSM121725", "GSM121726", "GSM121727", "GSM121728", "GSM121729", "GSM121730", "GSM121731", "GSM121732", "GSM121733", "GSM121734", "GSM121735", "GSM121736", "GSM121737", "GSM121738", "GSM121739", "GSM121740", "GSM121741", "GSM121742", "GSM121743", "GSM121744", "GSM121745", "GSM121746", "GSM121747", "GSM121748", "GSM121749", "GSM121750", "GSM121751", "GSM121752", "GSM121753", "GSM121754", "GSM121755", "GSM121756", "GSM121757", "GSM121758", "GSM121759", "GSM121760", "GSM121761", "GSM121762", "GSM121763", "GSM121764", "GSM121765", "GSM121766", "GSM121767", "GSM121768", "GSM121769", "GSM121770", "GSM121772", "GSM121773", "GSM121774", "GSM121775", "GSM121776", "GSM121777", "GSM121778", "GSM121779", "GSM121780", "GSM121781", "GSM121782", "GSM121783", "GSM121784", "GSM121785", "GSM121786", "GSM121787", "GSM121788", "GSM121789", "GSM121790", "GSM121791", "GSM121792", "GSM121793", "GSM121794", "GSM121795", "GSM121796", "GSM121797", "GSM121798", "GSM121799", "GSM121800", "GSM121801", "GSM121802", "GSM121803", "GSM121804", "GSM121805", "GSM121806", "GSM121807", "GSM121808", "GSM121809", "GSM121810", "GSM121811", "GSM121812", "GSM121813", "GSM121814", "GSM121815", "GSM121816", "GSM121817", "GSM121818", "GSM121819", "GSM121820", "GSM121821", "GSM121822", "GSM121823", "GSM121824", "GSM121825", "GSM121826", "GSM121827", "GSM121828", "GSM121829", "GSM121830", "GSM121831", "GSM121832", "GSM121833", "GSM121834", "GSM121835", "GSM121836", "GSM121837", "GSM121838", "GSM121839", "GSM121840", "GSM121841", "GSM121842", "GSM121843", "GSM121844", "GSM121845", "GSM121846", "GSM121847", "GSM121848", "GSM121849", "GSM121850", "GSM121851", "GSM121852", "GSM121853", "GSM121854", "GSM121855", "GSM121856", "GSM121857", "GSM121858", "GSM121859", "GSM121860", "GSM121861", "GSM121862", "GSM121863", "GSM121864", "GSM121865", "GSM121866", "GSM121867", "GSM121868", "GSM121869", "GSM121872", "GSM121873", "GSM121874", "GSM121875", "GSM121876", "GSM121877", "GSM121878", "GSM121879", "GSM121880", "GSM121881", "GSM121882", "GSM121883", "GSM121884", "GSM121885", "GSM121886", "GSM121887", "GSM121888", "GSM121889", "GSM121892", "GSM121893", "GSM121894", "GSM121895", "GSM121896", "GSM121897", "GSM121898", "GSM121899", "GSM121900", "GSM121901", "GSM121902", "GSM121903", "GSM121904", "GSM121905", "GSM121906", "GSM121907", "GSM121909", "GSM121917", "GSM121918", "GSM121919", "GSM121920", "GSM121921", "GSM121922", "GSM121923", "GSM121924", "GSM121925", "GSM121927", "GSM121928", "GSM121929", "GSM121930", "GSM121931", "GSM121932", "GSM121933", "GSM121934", "GSM121935", "GSM121936", "GSM121937", "GSM121938", "GSM121939", "GSM121940", "GSM121941", "GSM121942", "GSM121943", "GSM121944", "GSM121945", "GSM121946", "GSM121947", "GSM121950", "GSM121951", "GSM121952", "GSM121953", "GSM121954", "GSM121955", "GSM121956", "GSM121957", "GSM121958", "GSM121959", "GSM121960", "GSM121961", "GSM121962", "GSM121963", "GSM121964", "GSM121965", "GSM121966", "GSM121967", "GSM121968", "GSM121969", "GSM121970", "GSM121971", "GSM121972", "GSM121973", "GSM121974", "GSM121975", "GSM121976", "GSM121977", "GSM121978", "GSM121979", "GSM121980", "GSM121981", "GSM121982", "GSM121983", "GSM121984", "GSM121985", "GSM121986", "GSM121987", "GSM121988", "GSM121989", "GSM121990", "GSM121991", "GSM121992", "GSM121993", "GSM121994", "GSM121995", "GSM121996", "GSM121997", "GSM121998", "GSM121999", "GSM122000", "GSM122001", "GSM122002", "GSM122003", "GSM122004", "GSM122005", "GSM122006", "GSM122007", "GSM122008", "GSM122009", "GSM122010", "GSM122011", "GSM122012", "GSM122013", "GSM122014", "GSM122015", "GSM122016", "GSM122017", "GSM122018", "GSM122019", "GSM122020", "GSM122021", "GSM122022", "GSM122023", "GSM122024", "GSM122025", "GSM122026", "GSM122027", "GSM122028", "GSM122029"], "sample_count": 341, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "A Precisely Regulated Gene Expression Cassette Potently Modulates Metastasis and Survival in Multiple Solid Cancers", "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:GSE70947", "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=GSE70947", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE70947", "version": null, "note": "The data used to support the findings of this study are available from the GEO database (https://www.ncbi.nlm.nih. gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the GEO database (https://www.ncbi.nlm.nih. gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1823702", "GSM1823703", "GSM1823704", "GSM1823705", "GSM1823706", "GSM1823707", "GSM1823708", "GSM1823709", "GSM1823710", "GSM1823711", "GSM1823712", "GSM1823713", "GSM1823714", "GSM1823715", "GSM1823716", "GSM1823717", "GSM1823718", "GSM1823719", "GSM1823720", "GSM1823721", "GSM1823722", "GSM1823723", "GSM1823724", "GSM1823725", "GSM1823726", "GSM1823727", "GSM1823728", "GSM1823729", "GSM1823730", "GSM1823731", "GSM1823732", "GSM1823733", "GSM1823734", "GSM1823735", "GSM1823736", "GSM1823737", "GSM1823738", "GSM1823739", "GSM1823740", "GSM1823741", "GSM1823742", "GSM1823743", "GSM1823744", "GSM1823745", "GSM1823746", "GSM1823747", "GSM1823748", "GSM1823749", "GSM1823750", "GSM1823751", "GSM1823752", "GSM1823753", "GSM1823754", "GSM1823755", "GSM1823756", "GSM1823757", "GSM1823758", "GSM1823759", "GSM1823760", "GSM1823761", "GSM1823762", "GSM1823763", "GSM1823764", "GSM1823765", "GSM1823766", "GSM1823767", "GSM1823768", "GSM1823769", "GSM1823770", "GSM1823771", "GSM1823772", "GSM1823773", "GSM1823774", "GSM1823775", "GSM1823776", "GSM1823777", "GSM1823778", "GSM1823779", "GSM1823780", "GSM1823781", "GSM1823782", "GSM1823783", "GSM1823784", "GSM1823785", "GSM1823786", "GSM1823787", "GSM1823788", "GSM1823789", "GSM1823790", "GSM1823791", "GSM1823792", "GSM1823793", "GSM1823794", "GSM1823795", "GSM1823796", "GSM1823797", "GSM1823798", "GSM1823799", "GSM1823800", "GSM1823801", "GSM1823802", "GSM1823803", "GSM1823804", "GSM1823805", "GSM1823806", "GSM1823807", "GSM1823808", "GSM1823809", "GSM1823810", "GSM1823811", "GSM1823812", "GSM1823813", "GSM1823814", "GSM1823815", "GSM1823816", "GSM1823817", "GSM1823818", "GSM1823819", "GSM1823820", "GSM1823821", "GSM1823822", "GSM1823823", "GSM1823824", "GSM1823825", "GSM1823826", "GSM1823827", "GSM1823828", "GSM1823829", "GSM1823830", "GSM1823831", "GSM1823832", "GSM1823833", "GSM1823834", "GSM1823835", "GSM1823836", "GSM1823837", "GSM1823838", "GSM1823839", "GSM1823840", "GSM1823841", "GSM1823842", "GSM1823843", "GSM1823844", "GSM1823845", "GSM1823846", "GSM1823847", "GSM1823848", "GSM1823849", "GSM1823850", "GSM1823851", "GSM1823852", "GSM1823853", "GSM1823854", "GSM1823855", "GSM1823856", "GSM1823857", "GSM1823858", "GSM1823859", "GSM1823860", "GSM1823861", "GSM1823862", "GSM1823863", "GSM1823864", "GSM1823865", "GSM1823866", "GSM1823867", "GSM1823868", "GSM1823869", "GSM1823870", "GSM1823871", "GSM1823872", "GSM1823873", "GSM1823874", "GSM1823875", "GSM1823876", "GSM1823877", "GSM1823878", "GSM1823879", "GSM1823880", "GSM1823881", "GSM1823882", "GSM1823883", "GSM1823884", "GSM1823885", "GSM1823886", "GSM1823887", "GSM1823888", "GSM1823889", "GSM1823890", "GSM1823891", "GSM1823892", "GSM1823893", "GSM1823894", "GSM1823895", "GSM1823896", "GSM1823897", "GSM1823898", "GSM1823899", "GSM1823900", "GSM1823901", "GSM1823902", "GSM1823903", "GSM1823904", "GSM1823905", "GSM1823906", "GSM1823907", "GSM1823908", "GSM1823909", "GSM1823910", "GSM1823911", "GSM1823912", "GSM1823913", "GSM1823914", "GSM1823915", "GSM1823916", "GSM1823917", "GSM1823918", "GSM1823919", "GSM1823920", "GSM1823921", "GSM1823922", "GSM1823923", "GSM1823924", "GSM1823925", "GSM1823926", "GSM1823927", "GSM1823928", "GSM1823929", "GSM1823930", "GSM1823931", "GSM1823932", "GSM1823933", "GSM1823934", "GSM1823935", "GSM1823936", "GSM1823937", "GSM1823938", "GSM1823939", "GSM1823940", "GSM1823941", "GSM1823942", "GSM1823943", "GSM1823944", "GSM1823945", "GSM1823946", "GSM1823947", "GSM1823948", "GSM1823949", "GSM1823950", "GSM1823951", "GSM1823952", "GSM1823953", "GSM1823954", "GSM1823955", "GSM1823956", "GSM1823957", "GSM1823958", "GSM1823959", "GSM1823960", "GSM1823961", "GSM1823962", "GSM1823963", "GSM1823964", "GSM1823965", "GSM1823966", "GSM1823967", "GSM1823968", "GSM1823969", "GSM1823970", "GSM1823971", "GSM1823972", "GSM1823973", "GSM1823974", "GSM1823975", "GSM1823976", "GSM1823977", "GSM1823978", "GSM1823979", "GSM1823980", "GSM1823981", "GSM1823982", "GSM1823983", "GSM1823984", "GSM1823985", "GSM1823986", "GSM1823987", "GSM1823988", "GSM1823989", "GSM1823990", "GSM1823991", "GSM1823992", "GSM1823993", "GSM1823994", "GSM1823995", "GSM1823996", "GSM1823997"], "sample_count": 296, "group_sizes": null, "group_sizes_basis": null, "platform": "13607", "taxon": "Homo sapiens", "title": "Age and estrogen-dependent inflammation in breast adenocarcinoma and normal breast tissue [cohort_2]", "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:GSE86374", "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=GSE86374", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE86374", "version": null, "note": "The data used to support the findings of this study are available from the GEO database (https://www.ncbi.nlm.nih. gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the GEO database (https://www.ncbi.nlm.nih. gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2301021", "GSM2301022", "GSM2301023", "GSM2301024", "GSM2301025", "GSM2301026", "GSM2301027", "GSM2301028", "GSM2301029", "GSM2301030", "GSM2301031", "GSM2301032", "GSM2301033", "GSM2301034", "GSM2301035", "GSM2301036", "GSM2301037", "GSM2301038", "GSM2301039", "GSM2301040", "GSM2301041", "GSM2301042", "GSM2301043", "GSM2301044", "GSM2301045", "GSM2301046", "GSM2301047", "GSM2301048", "GSM2301049", "GSM2301050", "GSM2301051", "GSM2301052", "GSM2301053", "GSM2301054", "GSM2301055", "GSM2301056", "GSM2301057", "GSM2301058", "GSM2301059", "GSM2301060", "GSM2301061", "GSM2301062", "GSM2301063", "GSM2301064", "GSM2301065", "GSM2301066", "GSM2301067", "GSM2301068", "GSM2301069", "GSM2301070", "GSM2301071", "GSM2301072", "GSM2301073", "GSM2301074", "GSM2301075", "GSM2301076", "GSM2301077", "GSM2301078", "GSM2301079", "GSM2301080", "GSM2301081", "GSM2301082", "GSM2301083", "GSM2301084", "GSM2301085", "GSM2301086", "GSM2301087", "GSM2301088", "GSM2301089", "GSM2301090", "GSM2301091", "GSM2301092", "GSM2301093", "GSM2301094", "GSM2301095", "GSM2301096", "GSM2301097", "GSM2301098", "GSM2301099", "GSM2301100", "GSM2301101", "GSM2301102", "GSM2301103", "GSM2301104", "GSM2301105", "GSM2301106", "GSM2301107", "GSM2301108", "GSM2301109", "GSM2301110", "GSM2301111", "GSM2301112", "GSM2301113", "GSM2301114", "GSM2301115", "GSM2301116", "GSM2301117", "GSM2301118", "GSM2301119", "GSM2301120", "GSM2301121", "GSM2301122", "GSM2301123", "GSM2301124", "GSM2301125", "GSM2301126", "GSM2301127", "GSM2301128", "GSM2301129", "GSM2301130", "GSM2301131", "GSM2301132", "GSM2301133", "GSM2301134", "GSM2301135", "GSM2301136", "GSM2301137", "GSM2301138", "GSM2301139", "GSM2301140", "GSM2301141", "GSM2301142", "GSM2301143", "GSM2301144", "GSM2301145", "GSM2301146", "GSM2301147", "GSM2301148", "GSM2301149", "GSM2301150", "GSM2301151", "GSM2301152", "GSM2301153", "GSM2301154", "GSM2301155", "GSM2301156", "GSM2301157", "GSM2301158", "GSM2301159", "GSM2301160", "GSM2301161", "GSM2301162", "GSM2301163", "GSM2301164", "GSM2301165", "GSM2301166", "GSM2301167", "GSM2301168", "GSM2301169", "GSM2301170", "GSM2301171", "GSM2301172", "GSM2301173", "GSM2301174", "GSM2301175", "GSM2301176", "GSM2301177", "GSM2301178", "GSM2301179"], "sample_count": 159, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Analysis of somatic DNA copy number alterations and frequency of breast cancer intrinsic subtypes from Mexican women [gene expression]", "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:GSE5364 not downloaded", "asset:data:geo:GSE5364 licence not read", "asset:data:geo:GSE70947 not downloaded", "asset:data:geo:GSE70947 licence not read", "asset:data:geo:GSE86374 not downloaded", "asset:data:geo:GSE86374 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "KM"}}, {"id": "method-2", "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-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": "GO Enrichment"}}, {"id": "method-4", "family": null, "specific": null, "label": "Kaplan–Meier survival analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "reordered", "quote": "“KM is an online survival analysis tool to rapidly assess the effect of certain genes on cancer prognosis using microarray data”"}}], "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE86374", "GSE5364", "GSE70947"], "resolved_accessions": ["GSE86374", "GSE5364", "GSE70947"], "statements": ["The data used to support the findings of this study are available from the GEO database (https://www.ncbi.nlm.nih. gov/geo/)."], "basis": "The paper names GSE86374, GSE5364, GSE70947 in GEO database (Gene Expression Omnibus) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:33959662", "data:geo:GSE5364"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE5364"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:29:48Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 14904, "completion_tokens": 1641, "cached_tokens": 784}}, "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:33959662", "type": "paper", "label": "pmid:33959662"}, {"id": "source:pmid:33959662", "type": "manuscript", "label": "PMID 33959662 full text"}, {"id": "data:geo:GSE5364", "type": "dataset", "label": "GEO GSE5364"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33959662", "type": "paper", "label": "pmid:33959662"}, {"id": "source:pmid:33959662", "type": "manuscript", "label": "PMID 33959662 full text"}, {"id": "data:geo:GSE5364", "type": "dataset", "label": "GEO GSE5364"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33959662", "type": "extraction", "used": ["source:pmid:33959662"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE5364", "type": "accession_resolution", "used": ["data:geo:GSE5364"], "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:33959662", "parent_hash": "sha256:5892db4dd4662f488ce8f8800d0d5a6cc8cbd82a9473972bf46c93b78fb700da", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE5364 licence not read", "asset:data:geo:GSE5364 not downloaded", "asset:data:geo:GSE70947 licence not read", "asset:data:geo:GSE70947 not downloaded", "asset:data:geo:GSE86374 licence not read", "asset:data:geo:GSE86374 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["t of certain genes on cancer prognosis using microarray data (https://kmplot.com/analysis/index.php?"], "order_basis": "paper_text_order:3141", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["KM"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}