Prognostic and metabolic characteristics of a novel cuproptosis-related signature in patients with hepatocellular carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38259960", "kind": "science-record", "revision": 3, "content_hash": "sha256:0386f099d6e952c3217b5e54da9c0174a12807ab736563b0a72c1128a1e8135d", "created_at": "2026-11-01T19:20:11Z", "updated_at": "2026-11-01T22:11:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prognostic and metabolic characteristics of a novel cuproptosis-related signature in patients with hepatocellular carcinoma.", "doi": "10.1016/j.heliyon.2023.e23686", "pmid": "38259960", "authors": ["Xin Qu", "Ling-Cui Meng", "Xi Lu", "Xian Chen", "Yong Li", "Rui Zhou", "Yan-Juan Zhu", "Yi-Chang Luo", "Jin-Tao Huang", "Xiao-Liang Shi", "Hai-Bo Zhang"], "journal": "Heliyon", "year": 2024, "abstract": "Cuproptosis is a novel discovered mode of programmed cell death. To identify the molecular regulatory patterns related to cuproptosis, this study was designed for exploring the correlation between cuproptosis-related genes (CRGs) and the prognosis, metabolism, and treatment of hepatocellular carcinoma (HCC). Cancer Genome Atlas (TCGA) database was used to screen 363 HCC samples, which were categorized into 2 clusters based on the expression of CRGs. Survival analysis demonstrated that overall survival (OS) was better in Cluster 1 than Cluster 2 which might to be relevant to differences in metabolic based on functional analysis. With LASSO regression analysis and univariate COX regression, 8 prognosis-related genes were screened, a differently expressed genes (DEGs) were then constructed (HCC patients' DEGs)-based signature. The signature's stability was also validated in the 2 independent cohorts and test cohorts (GSE14520, HCC dataset in PCAWG). The 1-year, 3-year, and 5-year area under the curve (AUC) were 0.756, 0.706, and 0.722, respectively. The signature could also well predict the response to chemotherapy, targeted and transcatheter arterial chemoembolization (TACE) by providing a risk score. Moreover, the correlation was uncovered by the research between the metabolism and risk score. In conclusion, a unique cuproptosis-related signature that be capable of predicting patients' prognosis with HCC, and offered valuable insights into chemotherapy, TACE and targeted therapies for these patients has been developed.", "claims": [{"id": "claim-method", "statement": "With LASSO regression analysis and univariate COX regression, 8 prognosis-related genes were screened, a differently expressed genes (DEGs) were then constructed (HCC patients' DEGs)-based signature.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38259960", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "With LASSO regression analysis and univariate COX regression, 8 prognosis-related genes were screened, a differently expressed genes (DEGs) were then constructed (HCC patients' DEGs)-based signature."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data analyzed in this study were available from publicly online databases TCGA (https://portal.gdc.cancer.gov/), GEO (https://www.ncbi.nlm.nih.gov/geo/) and PCAWG (https://dcc.icgc.org/pcawg/). Information about each data set was presented in the manuscript.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38259960", "locator": "sections[20] \"Data availability\" paragraph 2", "quote": "All data analyzed in this study were available from publicly online databases TCGA (https://portal.gdc.cancer.gov/), GEO (https://www.ncbi.nlm.nih.gov/geo/) and PCAWG (https://dcc.icgc.org/pcawg/). Information about each data set was presented in the manuscript."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The cuproptosis-related prognostic signature predicted HCC prognosis with 1-, 3-, and 5-year AUC values of 0.756, 0.706, and 0.722, respectively.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38259960", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The 1-year, 3-year, and 5-year area under the curve (AUC) were 0.756, 0.706, and 0.722, respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The cuproptosis-related prognostic signature predicted HCC prognosis with 1-, 3-, and 5-year AUC values of 0.756, 0.706, and 0.722, respectively.", "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:38259960"], "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:GSE104580"], "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:GSE104580"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38259960", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.heliyon.2023.e23686", "sha256": "sha256:9e2ca398e46e7ecde83ff27e90632f46234eeee3f701f56132a1972a027651d9", "bytes": 30731, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.heliyon.2023.e23686", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10801206", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE104580", "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=GSE104580", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE104580", "version": null, "note": "All data analyzed in this study were available from publicly online databases TCGA (https://portal.gdc.cancer.gov/), GEO (https://www.ncbi.nlm.nih.gov/geo/) and PCAWG (https://dcc.icgc.org/pcawg/). Information about each data set was presented in the manuscript.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data analyzed in this study were available from publicly online databases TCGA (https://portal.gdc.cancer.gov/), GEO (https://www.ncbi.nlm.nih.gov/geo/) and PCAWG (https://dcc.icgc.org/pcawg/). Information about each data set was presented in the manuscript.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2803655", "GSM2803656", "GSM2803657", "GSM2803658", "GSM2803659", "GSM2803660", "GSM2803661", "GSM2803662", "GSM2803663", "GSM2803664", "GSM2803665", "GSM2803666", "GSM2803667", "GSM2803668", "GSM2803669", "GSM2803670", "GSM2803671", "GSM2803672", "GSM2803673", "GSM2803674", "GSM2803675", "GSM2803676", "GSM2803677", "GSM2803678", "GSM2803679", "GSM2803680", "GSM2803681", "GSM2803682", "GSM2803683", "GSM2803684", "GSM2803685", "GSM2803686", "GSM2803687", "GSM2803688", "GSM2803689", "GSM2803690", "GSM2803691", "GSM2803692", "GSM2803693", "GSM2803694", "GSM2803695", "GSM2803696", "GSM2803697", "GSM2803698", "GSM2803699", "GSM2803700", "GSM2803701", "GSM2803702", "GSM2803703", "GSM2803704", "GSM2803705", "GSM2803706", "GSM2803707", "GSM2803708", "GSM2803709", "GSM2803710", "GSM2803711", "GSM2803712", "GSM2803713", "GSM2803714", "GSM2803715", "GSM2803716", "GSM2803717", "GSM2803718", "GSM2803719", "GSM2803720", "GSM2803721", "GSM2803722", "GSM2803723", "GSM2803724", "GSM2803725", "GSM2803726", "GSM2803727", "GSM2803728", "GSM2803729", "GSM2803730", "GSM2803731", "GSM2803732", "GSM2803733", "GSM2803734", "GSM2803735", "GSM2803736", "GSM2803737", "GSM2803738", "GSM2803739", "GSM2803740", "GSM2803741", "GSM2803742", "GSM2803743", "GSM2803744", "GSM2803745", "GSM2803746", "GSM2803747", "GSM2803748", "GSM2803749", "GSM2803750", "GSM2803751", "GSM2803752", "GSM2803753", "GSM2803754", "GSM2803755", "GSM2803756", "GSM2803757", "GSM2803758", "GSM2803759", "GSM2803760", "GSM2803761", "GSM2803762", "GSM2803763", "GSM2803764", "GSM2803765", "GSM2803766", "GSM2803767", "GSM2803768", "GSM2803769", "GSM2803770", "GSM2803771", "GSM2803772", "GSM2803773", "GSM2803774", "GSM2803775", "GSM2803776", "GSM2803777", "GSM2803778", "GSM2803779", "GSM2803780", "GSM2803781", "GSM2803782", "GSM2803783", "GSM2803784", "GSM2803785", "GSM2803786", "GSM2803787", "GSM2803788", "GSM2803789", "GSM2803790", "GSM2803791", "GSM2803792", "GSM2803793", "GSM2803794", "GSM2803795", "GSM2803796", "GSM2803797", "GSM2803798", "GSM2803799", "GSM2803800", "GSM2803801"], "sample_count": 147, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Using a novel gene signature for predicting the efficacy of the transarterial chemoembolization in patients with hepatocellular carcinoma.", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE109211", "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=GSE109211", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE109211", "version": null, "note": "All data analyzed in this study were available from publicly online databases TCGA (https://portal.gdc.cancer.gov/), GEO (https://www.ncbi.nlm.nih.gov/geo/) and PCAWG (https://dcc.icgc.org/pcawg/). Information about each data set was presented in the manuscript.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data analyzed in this study were available from publicly online databases TCGA (https://portal.gdc.cancer.gov/), GEO (https://www.ncbi.nlm.nih.gov/geo/) and PCAWG (https://dcc.icgc.org/pcawg/). Information about each data set was presented in the manuscript.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2935278", "GSM2935279", "GSM2935280", "GSM2935281", "GSM2935282", "GSM2935283", "GSM2935284", "GSM2935285", "GSM2935286", "GSM2935287", "GSM2935288", "GSM2935289", "GSM2935290", "GSM2935291", "GSM2935292", "GSM2935293", "GSM2935294", "GSM2935295", "GSM2935296", "GSM2935297", "GSM2935298", "GSM2935299", "GSM2935300", "GSM2935301", "GSM2935302", "GSM2935303", "GSM2935304", "GSM2935305", "GSM2935306", "GSM2935307", "GSM2935308", "GSM2935309", "GSM2935310", "GSM2935311", "GSM2935312", "GSM2935313", "GSM2935314", "GSM2935315", "GSM2935316", "GSM2935317", "GSM2935318", "GSM2935319", "GSM2935320", "GSM2935321", "GSM2935322", "GSM2935323", "GSM2935324", "GSM2935325", "GSM2935326", "GSM2935327", "GSM2935328", "GSM2935329", "GSM2935330", "GSM2935331", "GSM2935332", "GSM2935333", "GSM2935334", "GSM2935335", "GSM2935336", "GSM2935337", "GSM2935338", "GSM2935339", "GSM2935340", "GSM2935341", "GSM2935342", "GSM2935343", "GSM2935344", "GSM2935345", "GSM2935346", "GSM2935347", "GSM2935348", "GSM2935349", "GSM2935350", "GSM2935351", "GSM2935352", "GSM2935353", "GSM2935354", "GSM2935355", "GSM2935356", "GSM2935357", "GSM2935358", "GSM2935359", "GSM2935360", "GSM2935361", "GSM2935362", "GSM2935363", "GSM2935364", "GSM2935365", "GSM2935366", "GSM2935367", "GSM2935368", "GSM2935369", "GSM2935370", "GSM2935371", "GSM2935372", "GSM2935373", "GSM2935374", "GSM2935375", "GSM2935376", "GSM2935377", "GSM2935378", "GSM2935379", "GSM2935380", "GSM2935381", "GSM2935382", "GSM2935383", "GSM2935384", "GSM2935385", "GSM2935386", "GSM2935387", "GSM2935388", "GSM2935389", "GSM2935390", "GSM2935391", "GSM2935392", "GSM2935393", "GSM2935394", "GSM2935395", "GSM2935396", "GSM2935397", "GSM2935398", "GSM2935399", "GSM2935400", "GSM2935401", "GSM2935402", "GSM2935403", "GSM2935404", "GSM2935405", "GSM2935406", "GSM2935407", "GSM2935408", "GSM2935409", "GSM2935410", "GSM2935411", "GSM2935412", "GSM2935413", "GSM2935414", "GSM2935415", "GSM2935416", "GSM2935417"], "sample_count": 140, "group_sizes": null, "group_sizes_basis": null, "platform": "13938", "taxon": "Homo sapiens", "title": "Molecular predictors of prevention of recurrence in hepatocellular carcinoma with sorafenib as adjuvant treatment in the phase 3 STORM trial", "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:GSE14520", "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=GSE14520", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14520", "version": null, "note": "All data analyzed in this study were available from publicly online databases TCGA (https://portal.gdc.cancer.gov/), GEO (https://www.ncbi.nlm.nih.gov/geo/) and PCAWG (https://dcc.icgc.org/pcawg/). Information about each data set was presented in the manuscript.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data analyzed in this study were available from publicly online databases TCGA (https://portal.gdc.cancer.gov/), GEO (https://www.ncbi.nlm.nih.gov/geo/) and PCAWG (https://dcc.icgc.org/pcawg/). Information about each data set was presented in the manuscript.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM362947", "GSM362948", "GSM362949", "GSM362950", "GSM362951", "GSM362952", "GSM362953", "GSM362954", "GSM362955", "GSM362956", "GSM362957", "GSM362958", "GSM362959", "GSM362960", "GSM362961", "GSM362962", "GSM362963", "GSM362964", "GSM362965", "GSM362966", "GSM362967", "GSM362968", "GSM362969", "GSM362970", "GSM362971", "GSM362972", "GSM362973", "GSM362974", "GSM362975", "GSM362976", "GSM362977", "GSM362978", "GSM362979", "GSM362980", "GSM362981", "GSM362982", "GSM362983", "GSM362984", "GSM362985", "GSM362986", "GSM362987", "GSM362988", "GSM362989", "GSM362990", "GSM362991", "GSM362992", "GSM362993", "GSM362994", "GSM362995", "GSM362996", "GSM362997", "GSM362998", "GSM362999", "GSM363000", "GSM363001", "GSM363002", "GSM363003", "GSM363004", "GSM363005", "GSM363006", "GSM363007", "GSM363008", "GSM363009", "GSM363010", "GSM363011", "GSM363012", "GSM363013", "GSM363014", "GSM363015", "GSM363016", "GSM363017", "GSM363018", "GSM363019", "GSM363020", "GSM363021", "GSM363022", "GSM363023", "GSM363024", "GSM363025", "GSM363026", "GSM363027", "GSM363028", "GSM363029", "GSM363030", "GSM363031", "GSM363032", "GSM363033", "GSM363034", "GSM363035", "GSM363036", "GSM363037", "GSM363038", "GSM363039", "GSM363040", "GSM363041", "GSM363042", "GSM363043", "GSM363044", "GSM363045", "GSM363046", "GSM363047", "GSM363048", "GSM363049", "GSM363050", "GSM363051", "GSM363052", "GSM363053", "GSM363054", "GSM363055", "GSM363056", "GSM363057", "GSM363058", "GSM363059", "GSM363060", "GSM363061", "GSM363062", "GSM363063", "GSM363064", "GSM363065", "GSM363066", "GSM363067", "GSM363068", "GSM363069", "GSM363070", "GSM363071", "GSM363072", "GSM363073", "GSM363074", "GSM363075", "GSM363076", "GSM363077", "GSM363078", "GSM363079", "GSM363080", "GSM363081", "GSM363082", "GSM363083", "GSM363084", "GSM363085", "GSM363086", "GSM363087", "GSM363088", "GSM363089", "GSM363090", "GSM363091", "GSM363092", "GSM363093", "GSM363094", "GSM363095", "GSM363096", "GSM363097", "GSM363098", "GSM363099", "GSM363100", "GSM363101", "GSM363102", "GSM363103", "GSM363104", "GSM363105", "GSM363106", "GSM363107", "GSM363108", "GSM363109", "GSM363110", "GSM363111", "GSM363112", "GSM363113", "GSM363114", "GSM363115", "GSM363116", "GSM363117", "GSM363118", "GSM363119", "GSM363120", "GSM363121", "GSM363122", "GSM363123", "GSM363124", "GSM363125", "GSM363126", "GSM363127", "GSM363128", "GSM363129", "GSM363130", "GSM363131", "GSM363132", "GSM363133", "GSM363134", "GSM363135", "GSM363136", "GSM363137", "GSM363138", "GSM363139", "GSM363140", "GSM363141", "GSM363142", "GSM363143", "GSM363144", "GSM363145", "GSM363146", "GSM363147", "GSM363148", "GSM363149", "GSM363150", "GSM363151", "GSM363152", "GSM363153", "GSM363154", "GSM363155", "GSM363156", "GSM363157", "GSM363158", "GSM363159", "GSM363160", "GSM363161", "GSM363162", "GSM363163", "GSM363164", "GSM363165", "GSM363166", "GSM363167", "GSM363168", "GSM363169", "GSM363170", "GSM363171", "GSM363172", "GSM363173", "GSM363174", "GSM363175", "GSM363176", "GSM363177", "GSM363178", "GSM363179", "GSM363180", "GSM363181", "GSM363182", "GSM363183", "GSM363184", "GSM363185", "GSM363186", "GSM363187", "GSM363188", "GSM363189", "GSM363190", "GSM363191", "GSM363192", "GSM363193", "GSM363194", "GSM363195", "GSM363196", "GSM363197", "GSM363198", "GSM363199", "GSM363200", "GSM363201", "GSM363202", "GSM363203", "GSM363204", "GSM363205", "GSM363206", "GSM363207", "GSM363208", "GSM363209", "GSM363210", "GSM363211", "GSM363212", "GSM363213", "GSM363214", "GSM363215", "GSM363216", "GSM363217", "GSM363218", "GSM363219", "GSM363220", "GSM363221", "GSM363222", "GSM363223", "GSM363224", "GSM363225", "GSM363226", "GSM363227", "GSM363228", "GSM363229", "GSM363230", "GSM363231", "GSM363232", "GSM363233", "GSM363234", "GSM363235", "GSM363236", "GSM363237", "GSM363238", "GSM363239", "GSM363240", "GSM363241", "GSM363242", "GSM363243", "GSM363244", "GSM363245", "GSM363246", "GSM363247", "GSM363248", "GSM363249", "GSM363250", "GSM363251", "GSM363252", "GSM363253", "GSM363254", "GSM363255", "GSM363256", "GSM363257", "GSM363258", "GSM363259", "GSM363260", "GSM363261", "GSM363262", "GSM363263", "GSM363264", "GSM363265", "GSM363266", "GSM363267", "GSM363268", "GSM363269", "GSM363270", "GSM363271", "GSM363272", "GSM363273", "GSM363274", "GSM363275", "GSM363276", "GSM363277", "GSM363278", "GSM363279", "GSM363280", "GSM363281", "GSM363282", "GSM363283", "GSM363284", "GSM363285", "GSM363286", "GSM363287", "GSM363288", "GSM363289", "GSM363290", "GSM363291", "GSM363292", "GSM363293", "GSM363294", "GSM363295", "GSM363296", "GSM363297", "GSM363298", "GSM363299", "GSM363300", "GSM363301", "GSM363302", "GSM363303", "GSM363304", "GSM363305", "GSM363306", "GSM363307", "GSM363308", "GSM363309", "GSM363310", "GSM363311", "GSM363312", "GSM363313", "GSM363314", "GSM363315", "GSM363316", "GSM363317", "GSM363318", "GSM363319", "GSM363320", "GSM363321", "GSM363322", "GSM363323", "GSM363324", "GSM363325", "GSM363326", "GSM363327", "GSM363328", "GSM363329", "GSM363330", "GSM363331", "GSM363332", "GSM363333", "GSM363334", "GSM363335", "GSM363336", "GSM363337", "GSM363338", "GSM363339", "GSM363340", "GSM363341", "GSM363342", "GSM363343", "GSM363344", "GSM363345", "GSM363346", "GSM363347", "GSM363348", "GSM363349", "GSM363350", "GSM363351", "GSM363352", "GSM363353", "GSM363354", "GSM363355", "GSM363356", "GSM363357", "GSM363358", "GSM363359", "GSM363360", "GSM363361", "GSM363362", "GSM363363", "GSM363364", "GSM363365", "GSM363366", "GSM363367", "GSM363368", "GSM363369", "GSM363370", "GSM363371", "GSM363372", "GSM363373", "GSM363374", "GSM363375", "GSM363376", "GSM363378", "GSM363380", "GSM363381", "GSM363382", "GSM363384", "GSM363386", "GSM363388", "GSM363391", "GSM363393", "GSM363397", "GSM363400", "GSM363402", "GSM363404", "GSM363407", "GSM363417", "GSM363420", "GSM363421", "GSM363422", "GSM363423", "GSM363424", "GSM363425", "GSM363426", "GSM363427", "GSM363428", "GSM363429", "GSM363430", "GSM363431", "GSM363432", "GSM363433", "GSM363434", "GSM363435", "GSM363436", "GSM363437", "GSM363438", "GSM363439", "GSM363440", "GSM363441", "GSM363442", "GSM363443", "GSM363444", "GSM363445", "GSM363446", "GSM363447", "GSM363448", "GSM363449", "GSM363450", "GSM363451", "GSM712532", "GSM712533", "GSM712534", "GSM712535", "GSM712536", "GSM712537", "GSM712538", "GSM712539", "GSM712540", "GSM712541", "GSM712542"], "sample_count": 488, "group_sizes": null, "group_sizes_basis": null, "platform": "3921;571", "taxon": "Homo sapiens", "title": "Gene expression data of human hepatocellular carcinoma (HCC)", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE104580 not downloaded", "asset:data:geo:GSE104580 licence not read", "asset:data:geo:GSE109211 not downloaded", "asset:data:geo:GSE109211 licence not read", "asset:data:geo:GSE14520 not downloaded", "asset:data:geo:GSE14520 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": "With LASSO regression analysis and univariate COX regression, 8 prognosis-related genes were screened, a differently expressed genes (DEGs) were then constructed (HCC patients' DEGs)-based signature."}}, {"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"}}, {"id": "method-3", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "PCA"}}, {"id": "method-4", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Spearman's rank correlation"}}, {"id": "method-5", "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": 0.8, "band": "high", "quote": "PPI"}}], "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": ["GSE14520", "GSE109211", "GSE104580"], "resolved_accessions": ["GSE14520", "GSE109211", "GSE104580"], "statements": ["All data analyzed in this study were available from publicly online databases TCGA (https://portal.gdc.cancer.gov/), GEO (https://www.ncbi.nlm.nih.gov/geo/) and PCAWG (https://dcc.icgc.org/pcawg/). Information about each data set was presented in the manuscript."], "basis": "The paper names GSE14520, GSE109211, GSE104580 in The GEO database 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:38259960", "data:geo:GSE104580"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE104580"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:06:15Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 8886, "completion_tokens": 1759, "cached_tokens": 128}}, "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:38259960", "type": "paper", "label": "pmid:38259960"}, {"id": "source:pmid:38259960", "type": "manuscript", "label": "PMID 38259960 full text"}, {"id": "data:geo:GSE104580", "type": "dataset", "label": "GEO GSE104580"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38259960", "type": "paper", "label": "pmid:38259960"}, {"id": "source:pmid:38259960", "type": "manuscript", "label": "PMID 38259960 full text"}, {"id": "data:geo:GSE104580", "type": "dataset", "label": "GEO GSE104580"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38259960", "type": "extraction", "used": ["source:pmid:38259960"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE104580", "type": "accession_resolution", "used": ["data:geo:GSE104580"], "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:38259960", "parent_hash": "sha256:630f2238a0aab7cc2abe95e14c53c6f52d4fcfa093c5fa8d2402f9f116f94ff1", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE104580 licence not read", "asset:data:geo:GSE104580 not downloaded", "asset:data:geo:GSE109211 licence not read", "asset:data:geo:GSE109211 not downloaded", "asset:data:geo:GSE14520 licence not read", "asset:data:geo:GSE14520 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": ["With LASSO regression analysis and univariate COX regression, 8 prognosis-related genes were screened, a differently expressed genes (DEGs) were then constructed (HCC patients' DEGs)-based signature."], "order_basis": "analysis_only", "id": "assay:1"}]}