Identification of senescence-related molecular subtypes and key genes for prostate cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36124532", "kind": "science-record", "revision": 5, "content_hash": "sha256:6d6f3df05fa6fd48d5812164c093a7737ae07eee688cb9c0870b0a1ea8da1de7", "created_at": "2026-11-01T18:15:23Z", "updated_at": "2026-11-01T22:50:07Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of senescence-related molecular subtypes and key genes for prostate cancer.", "doi": "10.4103/aja202258", "pmid": "36124532", "authors": ["De-Chao Feng", "Wei-Zhen Zhu", "Xu Shi", "Qiao Xiong", "Jia You", "Qiang Wei", "Lu Yang"], "journal": "Asian journal of andrology", "year": 2023, "abstract": "We identified distinct senescence-related molecular subtypes and critical genes among prostate cancer (PCa) patients undergoing radical prostatectomy (RP) or radical radiotherapy (RT). We conducted all analyses using R software and its suitable packages. Twelve genes, namely, secreted frizzled-related protein 4 (SFRP4), DNA topoisomerase II alpha (TOP2A), pleiotrophin (PTN), family with sequence similarity 107 member A (FAM107A), C-X-C motif chemokine ligand 14 (CXCL14), prostate androgen-regulated mucin-like protein 1 (PARM1), leucine zipper protein 2 (LUZP2), cluster of differentiation 38 (CD38), cartilage oligomeric matrix protein (COMP), vestigial-like family member 3 (VGLL3), apolipoprotein E (APOE), and aldehyde dehydrogenase 2 family member (ALDH2), were eventually used to subtype PCa patients from The Cancer Genome Atlas (TCGA) database and GSE116918, and the molecular subtypes showed good correlations with clinical features. In terms of the tumor immune environment (TME) analysis, compared with cluster 1, cancer-associated fibroblasts (CAFs) scored significantly higher, while endothelial cells scored lower in cluster 2 in TCGA database. There was a statistically significant correlation between both CAFs and endothelial cells with biochemical recurrence (BCR)-free survival for PCa patients undergoing RP. For the GSE116918 database, cluster 2 had significantly lower levels of CAFs and tumor purity and higher levels of stromal, immune, and Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE) scores than cluster 1; in addition, patients with high levels of CAFs, stromal scores, immune scores, and ESTIMATE scores and low levels of tumor purity tended to suffer from BCR. Based on the median of differentially expressed checkpoints, high expression of CD96, hepatitis A virus cellular receptor 2 (HAVCR2), and neuropilin 1 (NRP1) in GSE116918 and high expression of CD160 and tumor necrosis factor (ligand) superfamily member 18 (TNFSF18) in TCGA database were associated with a significantly higher risk of BCR than their counterparts. In conclusion, we first constructed distinct molecular subtypes and critical genes for PCa patients undergoing RP or RT from the fresh perspective of senescence.", "claims": [{"id": "claim-method", "statement": "The log-rank test was used to determine the DEGs related to BCR-free survival in TCGA database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36124532", "locator": "sections[2] \"MATERIALS AND METHODS\" paragraph 2", "quote": "The log-rank test was used to determine the DEGs related to BCR-free survival in TCGA database."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The standardized PCa data in The Cancer Genome Atlas (TCGA) database were downloaded from the University of California, Santa Cruz (UCSC) Xena (CA, USA),11 and the matrix of message RNA (mRNA) was extracted.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36124532", "locator": "sections[2] \"MATERIALS AND METHODS\" paragraph 2", "quote": "The standardized PCa data in The Cancer Genome Atlas (TCGA) database were downloaded from the University of California, Santa Cruz (UCSC) Xena (CA, USA),11 and the matrix of message RNA (mRNA) was extracted."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Patients in cluster 2 had a significantly higher risk of biochemical recurrence than patients in cluster 1 in both TCGA and GSE116918.", "kind": "quantitative", "target": {"value": 95.0, "unit": "per cent", "tolerance": null, "source": "In TCGA database, cluster 2 had a significantly higher risk of BCR than cluster 1 (hazard ratio [HR]: 2.20, 95% confidence interval [CI]: 1.31–3.69, P = 0.003; Figure 1d)."}, "evidence": [{"asset": "source:pmid:36124532", "locator": "sections[3] \"RESULTS\" paragraph 2", "quote": "In TCGA database, cluster 2 had a significantly higher risk of BCR than cluster 1 (hazard ratio [HR]: 2.20, 95% confidence interval [CI]: 1.31–3.69, P = 0.003; Figure 1d)."}, {"asset": "source:pmid:36124532", "locator": "sections[3] \"RESULTS\" paragraph 2", "quote": "Cluster 2 was more likely to encounter BCR (HR: 3.67, 95% CI: 2.14–6.29, P < 0.001; Figure 1e) and metastasis (HR: 5.93, 95% CI: 2.50–14.08, P = 0.006; Figure 1f) than cluster 1 in GSE116918."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Patients in cluster 2 had a significantly higher risk of biochemical recurrence than patients in cluster 1 in both TCGA and GSE116918.", "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:36124532"], "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:36124532", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.4103/aja202258", "sha256": "sha256:ad0942139dcd3f205e0049de6dfc7d0aadf9c7263429d0f469681b87bebcff96", "bytes": 34927, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.4103/aja202258", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10069687", "source": "europe_pmc_fulltext", "coverage": "whole_body", "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 standardized PCa data in The Cancer Genome Atlas (TCGA) database were downloaded from the University of California, Santa Cruz (UCSC) Xena (CA, USA),11 and the matrix of message RNA (mRNA) was extracted.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The standardized PCa data in The Cancer Genome Atlas (TCGA) database were downloaded from the University of California, Santa Cruz (UCSC) Xena (CA, USA),11 and the matrix of message RNA (mRNA) was extracted.", "access_statement_kind": "repository_route_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 standardized PCa data in The Cancer Genome Atlas (TCGA) database were downloaded from the University of California, Santa Cruz (UCSC) Xena (CA, USA),11 and the matrix of message RNA (mRNA) was extracted.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The standardized PCa data in The Cancer Genome Atlas (TCGA) database were downloaded from the University of California, Santa Cruz (UCSC) Xena (CA, USA),11 and the matrix of message RNA (mRNA) was extracted.", "access_statement_kind": "repository_route_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: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 standardized PCa data in The Cancer Genome Atlas (TCGA) database were downloaded from the University of California, Santa Cruz (UCSC) Xena (CA, USA),11 and the matrix of message RNA (mRNA) was extracted.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The standardized PCa data in The Cancer Genome Atlas (TCGA) database were downloaded from the University of California, Santa Cruz (UCSC) Xena (CA, USA),11 and the matrix of message RNA (mRNA) was extracted.", "access_statement_kind": "repository_route_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: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 standardized PCa data in The Cancer Genome Atlas (TCGA) database were downloaded from the University of California, Santa Cruz (UCSC) Xena (CA, USA),11 and the matrix of message RNA (mRNA) was extracted.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The standardized PCa data in The Cancer Genome Atlas (TCGA) database were downloaded from the University of California, Santa Cruz (UCSC) Xena (CA, USA),11 and the matrix of message RNA (mRNA) was extracted.", "access_statement_kind": "repository_route_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:GSE46602 not downloaded", "asset:data:geo:GSE46602 licence not read", "asset:data:geo:GSE62872 not downloaded", "asset:data:geo:GSE62872 licence not read"]}, "analysis": {"state": "partial", "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": "The log-rank test was used to determine the DEGs related to BCR-free survival in TCGA database."}}, {"id": "method-2", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-3", "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"}}, {"id": "method-4", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {"log2fc_threshold": "ed as absolute value of Log2FC (llogFCl) ≥0"}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "limma"}}, {"id": "method-5", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "Chi-square"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "chi_square_test", "expected_value": 95.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "gaps": ["method.reader_differs_from_extractor"]}, "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"], "resolved_accessions": ["GSE46602", "GSE32571", "GSE62872", "GSE116918"], "statements": ["The standardized PCa data in The Cancer Genome Atlas (TCGA) database were downloaded from the University of California, Santa Cruz (UCSC) Xena (CA, USA),11 and the matrix of message RNA (mRNA) was extracted."], "basis": "The paper names GSE46602, GSE32571, GSE62872, GSE116918 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": ["cox_ph"], "assets": ["source:pmid:36124532", "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": "2026-11-01T18:06:09Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 10647, "completion_tokens": 1913, "cached_tokens": 256}}, "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:36124532", "type": "paper", "label": "pmid:36124532"}, {"id": "source:pmid:36124532", "type": "manuscript", "label": "PMID 36124532 full text"}, {"id": "data:geo:GSE116918", "type": "dataset", "label": "GEO GSE116918"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36124532", "type": "paper", "label": "pmid:36124532"}, {"id": "source:pmid:36124532", "type": "manuscript", "label": "PMID 36124532 full text"}, {"id": "data:geo:GSE116918", "type": "dataset", "label": "GEO GSE116918"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36124532", "type": "extraction", "used": ["source:pmid:36124532"], "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:36124532", "parent_hash": "sha256:65d0c7514014f0163f45cf8eb58dea284dd5ad61a6f41a8480aaf806cee3d73b", "fork_of": null, "generation": 4}, "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:GSE46602 licence not read", "asset:data:geo:GSE46602 not downloaded", "asset:data:geo:GSE62872 licence not read", "asset:data:geo:GSE62872 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "methylation_array", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["g the Proportion of Immune and Cancer cells (EPIC) and Estimation of Stromal and Immune cells"], "order_basis": "paper_text_order:4540", "id": "assay:1"}, {"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": ["The log-rank test was used to determine the DEGs related to BCR-free survival in TCGA database."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}