Identification of circadian clock-related immunological prognostic index and molecular subtypes in prostate cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39259370", "kind": "science-record", "revision": 2, "content_hash": "sha256:c9cadbf8bf799ad818489540aa8765b9f5c5c9c9e8fdbfb67c2e67600140d21b", "created_at": "2026-11-01T20:29:24Z", "updated_at": "2026-11-01T21:33:52Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of circadian clock-related immunological prognostic index and molecular subtypes in prostate cancer.", "doi": "10.1007/s12672-024-01276-7", "pmid": "39259370", "authors": ["Lu Che", "Dengxiong Li", "Jie Wang", "Zhouting Tuo", "Koo Han Yoo", "Dechao Feng", "Yun Ou", "Ruicheng Wu", "Wuran Wei"], "journal": "Discover oncology", "year": 2024, "abstract": "BACKGROUND: Evidence suggests that the circadian clock (CIC) is among the important factors for tumorigenesis. We aimed to provide new insights into CIC-mediated molecular subtypes and gene prognostic indexes for prostate cancer (PCa) patients undergoing radical prostatectomy (RP) or radical radiotherapy (RT).\nMETHODS: PCa data from TCGA was analyzed to identify differentially expressed genes (DEGs) with significant fold changes and p-values. A prognostic index called CIC-related gene prognostic index (CICGPI) was developed through clustering methods and survival analysis and validated on multiple data sets. The diagnostic accuracy of CICGPI for resistance to chemotherapy and radiotherapy was confirmed. Additionally, the interaction between tumor immune environment and CICGPI score was explored, along with their correlation with prognosis.\nRESULTS: TOP2A, APOE, and ALDH2 were used to classify the PCa patients into two subtypes. Cluster 2 had a higher risk of biochemical recurrence (BCR) than cluster 1 for PCa patients undergoing RP or RT. A CIC-related gene prognostic index (CICGPI) was constructed using the above three genes for PCa patents in the TCGA database. The CICGPI score showed good prognostic value in the TCGA database and was externally confirmed by PCa patients in GSE116918, MSKCC2010 and GSE46602. In addition, the CICGPI score had a certain and high diagnostic accuracy for tumor chemoresistance (AUC: 0.781) and radioresistance (AUC: 0.988). For gene set variation analysis, we observed that both beta alanine metabolism and limonene and pinene degradation were upregulated in cluster 1 for PCa patients undergoing RP or RT. For PCa patients undergoing RP, cell cycle, homologous recombination, mismatch repair, and DNA replication were upregulated in cluster 2. A strongly positive relationship between cancer-related fibroblasts and CICGPI score was observed in PCa patients undergoing RP or RT. Moreover, a high density of CAFs was highly closely associated with poorer BCR-free survival of PCa patients.\nCONCLUSIONS: In this study, we established CIC-related immunological prognostic index and molecular subtypes, which might be useful for the clinical practice.", "claims": [{"id": "claim-method", "statement": "We used the clustered genes to establish a CIC-related gene prognostic index (CICGPI) through Cox regression analysis using PCa patients in TCGA.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39259370", "locator": "sections[3] \"Identifying key genes of molecular subtypes and prognostic index\" paragraph 3", "quote": "We used the clustered genes to establish a CIC-related gene prognostic index (CICGPI) through Cox regression analysis using PCa patients in TCGA."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The results showed here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39259370", "locator": "sections[15] \"notes\" paragraph 1", "quote": "The results showed here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga."}], "state": "complete"}, {"id": "claim-target-result", "statement": "In addition, the CICGPI score had a certain and high diagnostic accuracy for tumor chemoresistance (AUC: 0.781) and radioresistance (AUC: 0.988).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39259370", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "In addition, the CICGPI score had a certain and high diagnostic accuracy for tumor chemoresistance (AUC: 0.781) and radioresistance (AUC: 0.988)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "In addition, the CICGPI score had a certain and high diagnostic accuracy for tumor chemoresistance (AUC: 0.781) and radioresistance (AUC: 0.988).", "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:39259370"], "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:GSE116918"], "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:GSE116918"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39259370", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s12672-024-01276-7", "sha256": "sha256:fe9519513b751a2da75ad8a1961e9786702ea8c5ac82cfb2d99b91ef99d6c24b", "bytes": 41858, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s12672-024-01276-7", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11391008", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE116918", "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=GSE116918", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE116918", "version": null, "note": "The results showed here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The results showed here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3263664", "GSM3263665", "GSM3263666", "GSM3263667", "GSM3263668", "GSM3263669", "GSM3263670", "GSM3263671", "GSM3263672", "GSM3263673", "GSM3263674", "GSM3263675", "GSM3263676", "GSM3263677", "GSM3263678", "GSM3263679", "GSM3263680", "GSM3263681", "GSM3263682", "GSM3263683", "GSM3263684", "GSM3263685", "GSM3263686", "GSM3263687", "GSM3263688", "GSM3263689", "GSM3263690", "GSM3263691", "GSM3263692", "GSM3263693", "GSM3263694", "GSM3263695", "GSM3263696", "GSM3263697", "GSM3263698", "GSM3263699", "GSM3263700", "GSM3263701", "GSM3263702", "GSM3263703", "GSM3263704", "GSM3263705", "GSM3263706", "GSM3263707", "GSM3263708", "GSM3263709", "GSM3263710", "GSM3263711", "GSM3263712", "GSM3263713", "GSM3263714", "GSM3263715", "GSM3263716", "GSM3263717", "GSM3263718", "GSM3263719", "GSM3263720", "GSM3263721", "GSM3263722", "GSM3263723", "GSM3263724", "GSM3263725", "GSM3263726", "GSM3263727", "GSM3263728", "GSM3263729", "GSM3263730", "GSM3263731", "GSM3263732", "GSM3263733", "GSM3263734", "GSM3263735", "GSM3263736", "GSM3263737", "GSM3263738", "GSM3263739", "GSM3263740", "GSM3263741", "GSM3263742", "GSM3263743", "GSM3263744", "GSM3263745", "GSM3263746", "GSM3263747", "GSM3263748", "GSM3263749", "GSM3263750", "GSM3263751", "GSM3263752", "GSM3263753", "GSM3263754", "GSM3263755", "GSM3263756", "GSM3263757", "GSM3263758", "GSM3263759", "GSM3263760", "GSM3263761", "GSM3263762", "GSM3263763", "GSM3263764", "GSM3263765", "GSM3263766", "GSM3263767", "GSM3263768", "GSM3263769", "GSM3263770", "GSM3263771", "GSM3263772", "GSM3263773", "GSM3263774", "GSM3263775", "GSM3263776", "GSM3263777", "GSM3263778", "GSM3263779", "GSM3263780", "GSM3263781", "GSM3263782", "GSM3263783", "GSM3263784", "GSM3263785", "GSM3263786", "GSM3263787", "GSM3263788", "GSM3263789", "GSM3263790", "GSM3263791", "GSM3263792", "GSM3263793", "GSM3263794", "GSM3263795", "GSM3263796", "GSM3263797", "GSM3263798", "GSM3263799", "GSM3263800", "GSM3263801", "GSM3263802", "GSM3263803", "GSM3263804", "GSM3263805", "GSM3263806", "GSM3263807", "GSM3263808", "GSM3263809", "GSM3263810", "GSM3263811", "GSM3263812", "GSM3263813", "GSM3263814", "GSM3263815", "GSM3263816", "GSM3263817", "GSM3263818", "GSM3263819", "GSM3263820", "GSM3263821", "GSM3263822", "GSM3263823", "GSM3263824", "GSM3263825", "GSM3263826", "GSM3263827", "GSM3263828", "GSM3263829", "GSM3263830", "GSM3263831", "GSM3263832", "GSM3263833", "GSM3263834", "GSM3263835", "GSM3263836", "GSM3263837", "GSM3263838", "GSM3263839", "GSM3263840", "GSM3263841", "GSM3263842", "GSM3263843", "GSM3263844", "GSM3263845", "GSM3263846", "GSM3263847", "GSM3263848", "GSM3263849", "GSM3263850", "GSM3263851", "GSM3263852", "GSM3263853", "GSM3263854", "GSM3263855", "GSM3263856", "GSM3263857", "GSM3263858", "GSM3263859", "GSM3263860", "GSM3263861", "GSM3263862", "GSM3263863", "GSM3263864", "GSM3263865", "GSM3263866", "GSM3263867", "GSM3263868", "GSM3263869", "GSM3263870", "GSM3263871", "GSM3263872", "GSM3263873", "GSM3263874", "GSM3263875", "GSM3263876", "GSM3263877", "GSM3263878", "GSM3263879", "GSM3263880", "GSM3263881", "GSM3263882", "GSM3263883", "GSM3263884", "GSM3263885", "GSM3263886", "GSM3263887", "GSM3263888", "GSM3263889", "GSM3263890", "GSM3263891", "GSM3263892", "GSM3263893", "GSM3263894", "GSM3263895", "GSM3263896", "GSM3263897", "GSM3263898", "GSM3263899", "GSM3263900", "GSM3263901", "GSM3263902", "GSM3263903", "GSM3263904", "GSM3263905", "GSM3263906", "GSM3263907", "GSM3263908", "GSM3263909", "GSM3263910", "GSM3263911"], "sample_count": 248, "group_sizes": null, "group_sizes_basis": null, "platform": "25318", "taxon": "Homo sapiens", "title": "Using biopsies to improve risk stratification in patients with prostate cancer treated with radical radiation therapy", "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:GSE32571", "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=GSE32571", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE32571", "version": null, "note": "The results showed here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The results showed here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM807224", "GSM807225", "GSM807226", "GSM807227", "GSM807228", "GSM807229", "GSM807230", "GSM807231", "GSM807232", "GSM807233", "GSM807234", "GSM807235", "GSM807236", "GSM807237", "GSM807238", "GSM807239", "GSM807240", "GSM807241", "GSM807242", "GSM807243", "GSM807244", "GSM807245", "GSM807246", "GSM807247", "GSM807248", "GSM807249", "GSM807250", "GSM807251", "GSM807252", "GSM807253", "GSM807254", "GSM807255", "GSM807256", "GSM807257", "GSM807258", "GSM807259", "GSM807260", "GSM807261", "GSM807262", "GSM807263", "GSM807264", "GSM807265", "GSM807266", "GSM807267", "GSM807268", "GSM807269", "GSM807270", "GSM807271", "GSM807272", "GSM807273", "GSM807274", "GSM807275", "GSM807276", "GSM807277", "GSM807278", "GSM807279", "GSM807280", "GSM807281", "GSM807282", "GSM807283", "GSM807284", "GSM807285", "GSM807286", "GSM807287", "GSM807288", "GSM807289", "GSM807290", "GSM807291", "GSM807292", "GSM807293", "GSM807294", "GSM807295", "GSM807296", "GSM807297", "GSM807298", "GSM807299", "GSM807300", "GSM807301", "GSM807302", "GSM807303", "GSM807304", "GSM807305", "GSM807306", "GSM807307", "GSM807308", "GSM807309", "GSM807310", "GSM807311", "GSM807312", "GSM807313", "GSM807314", "GSM807315", "GSM807316", "GSM807317", "GSM807318", "GSM807319", "GSM807320", "GSM807321"], "sample_count": 98, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Gene signatures in prostate cancer linked to the Gleason score", "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:GSE42913", "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=GSE42913", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE42913", "version": null, "note": "The results showed here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The results showed here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1053293", "GSM1053294", "GSM1053295", "GSM1053296", "GSM1053297", "GSM1053298", "GSM1053299", "GSM1053300", "GSM1053301", "GSM1053302", "GSM1053303", "GSM1053304", "GSM1053305", "GSM1053306", "GSM1053307", "GSM1053308", "GSM1053309", "GSM1053310", "GSM1053311", "GSM1053312", "GSM1053313", "GSM1053314", "GSM1053315", "GSM1053316", "GSM1053317", "GSM1053318", "GSM1053319", "GSM1053320", "GSM1053321", "GSM1053322", "GSM1053323"], "sample_count": 31, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "A comprehensive gene expression analysis of resistance formation upon metronomic cyclophosphamide therapy", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE46602", "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=GSE46602", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE46602", "version": null, "note": "The results showed here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The results showed here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1133136", "GSM1133137", "GSM1133138", "GSM1133139", "GSM1133140", "GSM1133141", "GSM1133142", "GSM1133143", "GSM1133144", "GSM1133145", "GSM1133146", "GSM1133147", "GSM1133148", "GSM1133149", "GSM1133150", "GSM1133151", "GSM1133152", "GSM1133153", "GSM1133154", "GSM1133155", "GSM1133156", "GSM1133157", "GSM1133158", "GSM1133159", "GSM1133160", "GSM1133161", "GSM1133162", "GSM1133163", "GSM1133164", "GSM1133165", "GSM1133166", "GSM1133167", "GSM1133168", "GSM1133169", "GSM1133170", "GSM1133171", "GSM1133172", "GSM1133173", "GSM1133174", "GSM1133175", "GSM1133176", "GSM1133177", "GSM1133178", "GSM1133179", "GSM1133180", "GSM1133181", "GSM1133182", "GSM1133183", "GSM1133184", "GSM1133185"], "sample_count": 50, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from prostate cancer and benign prostate glands", "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:GSE53902", "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=GSE53902", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE53902", "version": null, "note": "The results showed here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The results showed here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1303309", "GSM1303310", "GSM1303311", "GSM1303312", "GSM1303313", "GSM1303314", "GSM1303315", "GSM1303316", "GSM1303317", "GSM1303318", "GSM1303319", "GSM1303320", "GSM1303321", "GSM1303322", "GSM1303323", "GSM1303324", "GSM1303325", "GSM1303326"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "16699", "taxon": "Homo sapiens", "title": "Comparative analysis of gene expression of radioresistant prostate cancer cells and prostate cancer progenitors", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE62872", "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=GSE62872", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62872", "version": null, "note": "The results showed here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The results showed here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1534793", "GSM1534794", "GSM1534795", "GSM1534796", "GSM1534797", "GSM1534798", "GSM1534799", "GSM1534800", "GSM1534801", "GSM1534802", "GSM1534803", "GSM1534804", "GSM1534805", "GSM1534806", "GSM1534807", "GSM1534808", "GSM1534809", "GSM1534810", "GSM1534811", "GSM1534812", "GSM1534813", "GSM1534814", "GSM1534815", "GSM1534816", "GSM1534817", "GSM1534818", "GSM1534819", "GSM1534820", "GSM1534821", "GSM1534822", "GSM1534823", "GSM1534824", "GSM1534825", "GSM1534826", "GSM1534827", "GSM1534828", "GSM1534829", "GSM1534830", "GSM1534831", "GSM1534832", "GSM1534833", "GSM1534834", "GSM1534835", "GSM1534836", "GSM1534837", "GSM1534838", "GSM1534839", "GSM1534840", "GSM1534841", "GSM1534842", "GSM1534843", "GSM1534844", "GSM1534845", "GSM1534846", "GSM1534847", "GSM1534848", "GSM1534849", "GSM1534850", "GSM1534851", "GSM1534852", "GSM1534853", "GSM1534854", "GSM1534855", "GSM1534856", "GSM1534857", "GSM1534858", "GSM1534859", "GSM1534860", "GSM1534861", "GSM1534862", "GSM1534863", "GSM1534864", "GSM1534865", "GSM1534866", "GSM1534867", "GSM1534868", "GSM1534869", "GSM1534870", "GSM1534871", "GSM1534872", "GSM1534873", "GSM1534874", "GSM1534875", "GSM1534876", "GSM1534877", "GSM1534878", "GSM1534879", "GSM1534880", "GSM1534881", "GSM1534882", "GSM1534883", "GSM1534884", "GSM1534885", "GSM1534886", "GSM1534887", "GSM1534888", "GSM1534889", "GSM1534890", "GSM1534891", "GSM1534892", "GSM1534893", "GSM1534894", "GSM1534895", "GSM1534896", "GSM1534897", "GSM1534898", "GSM1534899", "GSM1534900", "GSM1534901", "GSM1534902", "GSM1534903", "GSM1534904", "GSM1534905", "GSM1534906", "GSM1534907", "GSM1534908", "GSM1534909", "GSM1534910", "GSM1534911", "GSM1534912", "GSM1534913", "GSM1534914", "GSM1534915", "GSM1534916", "GSM1534917", "GSM1534918", "GSM1534919", "GSM1534920", "GSM1534921", "GSM1534922", "GSM1534923", "GSM1534924", "GSM1534925", "GSM1534926", "GSM1534927", "GSM1534928", "GSM1534929", "GSM1534930", "GSM1534931", "GSM1534932", "GSM1534933", "GSM1534934", "GSM1534935", "GSM1534936", "GSM1534937", "GSM1534938", "GSM1534939", "GSM1534940", "GSM1534941", "GSM1534942", "GSM1534943", "GSM1534944", "GSM1534945", "GSM1534946", "GSM1534947", "GSM1534948", "GSM1534949", "GSM1534950", "GSM1534951", "GSM1534952", "GSM1534953", "GSM1534954", "GSM1534955", "GSM1534956", "GSM1534957", "GSM1534958", "GSM1534959", "GSM1534960", "GSM1534961", "GSM1534962", "GSM1534963", "GSM1534964", "GSM1534965", "GSM1534966", "GSM1534967", "GSM1534968", "GSM1534969", "GSM1534970", "GSM1534971", "GSM1534972", "GSM1534973", "GSM1534974", "GSM1534975", "GSM1534976", "GSM1534977", "GSM1534978", "GSM1534979", "GSM1534980", "GSM1534981", "GSM1534982", "GSM1534983", "GSM1534984", "GSM1534985", "GSM1534986", "GSM1534987", "GSM1534988", "GSM1534989", "GSM1534990", "GSM1534991", "GSM1534992", "GSM1534993", "GSM1534994", "GSM1534995", "GSM1534996", "GSM1534997", "GSM1534998", "GSM1534999", "GSM1535000", "GSM1535001", "GSM1535002", "GSM1535003", "GSM1535004", "GSM1535005", "GSM1535006", "GSM1535007", "GSM1535008", "GSM1535009", "GSM1535010", "GSM1535011", "GSM1535012", "GSM1535013", "GSM1535014", "GSM1535015", "GSM1535016", "GSM1535017", "GSM1535018", "GSM1535019", "GSM1535020", "GSM1535021", "GSM1535022", "GSM1535023", "GSM1535024", "GSM1535025", "GSM1535026", "GSM1535027", "GSM1535028", "GSM1535029", "GSM1535030", "GSM1535031", "GSM1535032", "GSM1535033", "GSM1535034", "GSM1535035", "GSM1535036", "GSM1535037", "GSM1535038", "GSM1535039", "GSM1535040", "GSM1535041", "GSM1535042", "GSM1535043", "GSM1535044", "GSM1535045", "GSM1535046", "GSM1535047", "GSM1535048", "GSM1535049", "GSM1535050", "GSM1535051", "GSM1535052", "GSM1535053", "GSM1535054", "GSM1535055", "GSM1535056", "GSM1535057", "GSM1535058", "GSM1535059", "GSM1535060", "GSM1535061", "GSM1535062", "GSM1535063", "GSM1535064", "GSM1535065", "GSM1535066", "GSM1535067", "GSM1535068", "GSM1535069", "GSM1535070", "GSM1535071", "GSM1535072", "GSM1535073", "GSM1535074", "GSM1535075", "GSM1535076", "GSM1535077", "GSM1535078", "GSM1535079", "GSM1535080", "GSM1535081", "GSM1535082", "GSM1535083", "GSM1535084", "GSM1535085", "GSM1535086", "GSM1535087", "GSM1535088", "GSM1535089", "GSM1535090", "GSM1535091", "GSM1535092", "GSM1535093", "GSM1535094", "GSM1535095", "GSM1535096", "GSM1535097", "GSM1535098", "GSM1535099", "GSM1535100", "GSM1535101", "GSM1535102", "GSM1535103", "GSM1535104", "GSM1535105", "GSM1535106", "GSM1535107", "GSM1535108", "GSM1535109", "GSM1535110", "GSM1535111", "GSM1535112", "GSM1535113", "GSM1535114", "GSM1535115", "GSM1535116", "GSM1535117", "GSM1535118", "GSM1535119", "GSM1535120", "GSM1535121", "GSM1535122", "GSM1535123", "GSM1535124", "GSM1535125", "GSM1535126", "GSM1535127", "GSM1535128", "GSM1535129", "GSM1535130", "GSM1535131", "GSM1535132", "GSM1535133", "GSM1535134", "GSM1535135", "GSM1535136", "GSM1535137", "GSM1535138", "GSM1535139", "GSM1535140", "GSM1535141", "GSM1535142", "GSM1535143", "GSM1535144", "GSM1535145", "GSM1535146", "GSM1535147", "GSM1535148", "GSM1535149", "GSM1535150", "GSM1535151", "GSM1535152", "GSM1535153", "GSM1535154", "GSM1535155", "GSM1535156", "GSM1535157", "GSM1535158", "GSM1535159", "GSM1535160", "GSM1535161", "GSM1535162", "GSM1535163", "GSM1535164", "GSM1535165", "GSM1535166", "GSM1535167", "GSM1535168", "GSM1535169", "GSM1535170", "GSM1535171", "GSM1535172", "GSM1535173", "GSM1535174", "GSM1535175", "GSM1535176", "GSM1535177", "GSM1535178", "GSM1535179", "GSM1535180", "GSM1535181", "GSM1535182", "GSM1535183", "GSM1535184", "GSM1535185", "GSM1535186", "GSM1535187", "GSM1535188", "GSM1535189", "GSM1535190", "GSM1535191", "GSM1535192", "GSM1535193", "GSM1535194", "GSM1535195", "GSM1535196", "GSM1535197", "GSM1535198", "GSM1535199", "GSM1535200", "GSM1535201", "GSM1535202", "GSM1535203", "GSM1535204", "GSM1535205", "GSM1535206", "GSM1535207", "GSM1535208", "GSM1535209", "GSM1535210", "GSM1535211", "GSM1535212", "GSM1535213", "GSM1535214", "GSM1535215", "GSM1535216"], "sample_count": 424, "group_sizes": null, "group_sizes_basis": null, "platform": "19370", "taxon": "Homo sapiens", "title": "Association of Prostate Cancer Risk Variants with Gene Expression in Normal and Tumor Tissue", "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:GSE116918 not downloaded", "asset:data:geo:GSE116918 licence not read", "asset:data:geo:GSE32571 not downloaded", "asset:data:geo:GSE32571 licence not read", "asset:data:geo:GSE42913 not downloaded", "asset:data:geo:GSE42913 licence not read", "asset:data:geo:GSE46602 not downloaded", "asset:data:geo:GSE46602 licence not read", "asset:data:geo:GSE53902 not downloaded", "asset:data:geo:GSE53902 licence not read", "asset:data:geo:GSE62872 not downloaded", "asset:data:geo:GSE62872 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We used the clustered genes to establish a CIC-related gene prognostic index (CICGPI) through Cox regression analysis using PCa patients in TCGA."}}, {"id": "method-2", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}], "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE46602", "GSE32571", "GSE62872", "GSE116918", "GSE42913", "GSE53902"], "resolved_accessions": ["GSE46602", "GSE32571", "GSE62872", "GSE116918", "GSE42913", "GSE53902"], "statements": ["The results showed here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga."], "basis": "The paper names GSE46602, GSE32571, GSE62872, GSE116918, GSE42913, GSE53902 in Gene Expression Omnibus and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:39259370", "data:geo:GSE116918"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE116918"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:30:55Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11658, "completion_tokens": 2264, "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:39259370", "type": "paper", "label": "pmid:39259370"}, {"id": "source:pmid:39259370", "type": "manuscript", "label": "PMID 39259370 full text"}, {"id": "data:geo:GSE116918", "type": "dataset", "label": "GEO GSE116918"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39259370", "type": "paper", "label": "pmid:39259370"}, {"id": "source:pmid:39259370", "type": "manuscript", "label": "PMID 39259370 full text"}, {"id": "data:geo:GSE116918", "type": "dataset", "label": "GEO GSE116918"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39259370", "type": "extraction", "used": ["source:pmid:39259370"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE116918", "type": "accession_resolution", "used": ["data:geo:GSE116918"], "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:39259370", "parent_hash": "sha256:7d207ba3dd2a0c303ccd5df75134fc47fabdabcadeb844df9cf101407732bd65", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE116918 licence not read", "asset:data:geo:GSE116918 not downloaded", "asset:data:geo:GSE32571 licence not read", "asset:data:geo:GSE32571 not downloaded", "asset:data:geo:GSE42913 licence not read", "asset:data:geo:GSE42913 not downloaded", "asset:data:geo:GSE46602 licence not read", "asset:data:geo:GSE46602 not downloaded", "asset:data:geo:GSE53902 licence not read", "asset:data:geo:GSE53902 not downloaded", "asset:data:geo:GSE62872 licence not read", "asset:data:geo:GSE62872 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We used the clustered genes to establish a CIC-related gene prognostic index (CICGPI) through Cox regression analysis using PCa patients in TCGA."], "order_basis": "analysis_only", "id": "assay:1"}]}