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pmid:30243023
A new risk score based on twelve hepatocellular carcinoma-specific gene expression can predict the patients' prognosis.
Ting Lin · Jingxian Gu · Kai Qu · Xing Zhang · Xiaohua Ma · Runchen Miao · Xiaohong Xiang · Yunong Fu · Wenquan Niu · Junjun She · Chang Liu
Aging · 2018 doi:10.18632/aging.101563
Paper
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Experiment
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Data
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Analysis
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Execution
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Complete file
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We here generated a genetic risk score system comprised of 12 HCC-specific genes to better predict the prognosis of HCC patients. Four genomics profiling datasets (GSE5851, GSE28691, GSE15765 and GSE14323) were searched to seek HCC-specific genes by comparisons between cancer samples and normal liver tissues and between different subtypes of hepatic neoplasms. Univariate survival analysis screened HCC-specific genes associated with overall survival (OS) in the training dataset for next-step risk model construction. The prognostic value of the constructed HCC risk score system was then validated in the TCGA dataset. Stratified analysis indicated this scoring system showed better performance in elderly male patients with HBV infection and preoperative lower levels of creatinine, alpha-fetoprotein and platelet and higher level of albumin. 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"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}}, {"id": "data:geo:GSE15765", "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=GSE15765", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE15765", "version": null, "note": "We selected 75 CRCLM samples from GSE5851 (61) and GSE28691 (14), 70 HCC samples and 13 ICC samples from GSE15765 and 19 normal liver tissue samples from GSE14323 for integrated normalization and analysis.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We selected 75 CRCLM samples from GSE5851 (61) and GSE28691 (14), 70 HCC samples and 13 ICC samples from GSE15765 and 19 normal liver tissue samples from GSE14323 for integrated normalization and analysis.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM395647", "GSM395648", "GSM395649", "GSM395650", "GSM395651", "GSM395652", "GSM395653", "GSM395654", "GSM395655", "GSM395656", "GSM395657", "GSM395658", "GSM395659", "GSM395660", "GSM395661", "GSM395662", "GSM395663", "GSM395664", "GSM395665", "GSM395666", "GSM395667", "GSM395669", "GSM395670", "GSM395671", "GSM395672", "GSM395673", "GSM395674", "GSM395675", "GSM395676", "GSM395677", "GSM395678", "GSM395679", "GSM395680", "GSM395681", "GSM395682", "GSM395683", "GSM395684", "GSM395685", "GSM395686", "GSM395687", "GSM395688", "GSM395689", "GSM395690", "GSM395691", "GSM395692", "GSM395693", "GSM395694", "GSM395695", "GSM395696", "GSM395697", "GSM395698", "GSM395699", "GSM395700", "GSM395701", "GSM395702", "GSM395703", "GSM395704", "GSM395705", "GSM395706", "GSM395707", "GSM395708", "GSM395709", "GSM395710", "GSM395711", "GSM395712", "GSM395713", "GSM395714", "GSM395715", 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"identifier": "GSE28691", "version": null, "note": "We selected 75 CRCLM samples from GSE5851 (61) and GSE28691 (14), 70 HCC samples and 13 ICC samples from GSE15765 and 19 normal liver tissue samples from GSE14323 for integrated normalization and analysis.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We selected 75 CRCLM samples from GSE5851 (61) and GSE28691 (14), 70 HCC samples and 13 ICC samples from GSE15765 and 19 normal liver tissue samples from GSE14323 for integrated normalization and analysis.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM710556", "GSM710557", "GSM710558", "GSM710559", "GSM710560", "GSM710561", "GSM710562", "GSM710563", "GSM710564", "GSM710565", "GSM710566", "GSM710567", "GSM710568", "GSM710569", "GSM710570", "GSM710572", "GSM710573", "GSM710574", "GSM710575", "GSM710576", "GSM710577", "GSM710578", "GSM710579", "GSM710580", "GSM710581", "GSM710582", "GSM710583", 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GSE5851 (61) and GSE28691 (14), 70 HCC samples and 13 ICC samples from GSE15765 and 19 normal liver tissue samples from GSE14323 for integrated normalization and analysis.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We selected 75 CRCLM samples from GSE5851 (61) and GSE28691 (14), 70 HCC samples and 13 ICC samples from GSE15765 and 19 normal liver tissue samples from GSE14323 for integrated normalization and analysis.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM136578", "GSM136579", "GSM136580", "GSM136581", "GSM136582", "GSM136583", "GSM136584", "GSM136585", "GSM136586", "GSM136587", "GSM136588", "GSM136589", "GSM136590", "GSM136591", "GSM136592", "GSM136593", "GSM136594", "GSM136595", "GSM136596", "GSM136597", "GSM136598", "GSM136599", "GSM136600", "GSM136601", "GSM136602", "GSM136603", "GSM136604", "GSM136605", "GSM136606", "GSM136607", "GSM136608", "GSM136609", "GSM136610", "GSM136611", "GSM136612", "GSM136613", "GSM136614", "GSM136615", "GSM136616", "GSM136617", "GSM136618", "GSM136619", "GSM136620", "GSM136621", "GSM136622", "GSM136623", "GSM136624", "GSM136625", "GSM136626", "GSM136627", "GSM136628", "GSM136629", "GSM136630", "GSM136631", "GSM136632", "GSM136633", "GSM136634", "GSM136635", "GSM136636", "GSM136637", "GSM136638", "GSM136639", "GSM136640", "GSM136641", "GSM136642", "GSM136643", "GSM136644", "GSM136645", "GSM136646", "GSM136647", "GSM136648", "GSM136649", "GSM136650", "GSM136651", "GSM136652", "GSM136653", "GSM136654", "GSM136655", "GSM136656", "GSM136657"], "sample_count": 80, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "Phase II exploratory pharmacogenomics study of cetuximab monotherapy in patients with advanced metastatic CRC", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:30243023:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:cefdcc1030c74c413c8ca3dc88583a6563e558c76c1bdf638d2209deb3d339af", "bytes": 1593, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#t1", "version": null, "note": "Univariate/multivariate Cox regression analysis of clinicopathologic factors associated with OS in TCGA cohort.", "structure": {"pmcid": "PMC6188480", "section_index": 5, "section_title": "Validation and development of 12 HCC-specific gene signature for prognosis", "row_count": 18, "column_count": 6}, "table": {"label": "Table 1", "caption": "Univariate/multivariate Cox regression analysis of clinicopathologic factors associated with OS in TCGA cohort.", "rows": [["Variables", "Univariate analysis", "", "Multivariate analysis"], ["HR (95% CI)", "P value", "", "HR (95% CI)", "P value"], ["Risk score (> 8.9/≤ 8.9)", "1.910(1.250-2.919)", "0.003*", "", "1.617(1.021-2.560)", "0.040*"], ["TNM stage (I/II/III/IV)", "1.282(0.993-1.655)", "0.057", "", "—", "—"], ["Hepatitis (HBV/HCV/neither)", "0.751(0.527-1.069)", "0.112", "", "—", "—"], ["Alcohol consumption (yes/no)", "0.835(0.514-1.359)", "0.469", "", "—", "—"], ["Gender (female/male)", "0.773(0.504-1.185)", "0.237", "", "—", "—"], ["Age (>50/≤50)", "1.967(1.043-3.710)", "0.037*", "", "1.454(0.711-2.971)", "0.305"], ["Cirrhosis (yes/no)", "0.865(0.471-1.587)", "0.639", "", "—", "—"], ["Albumin (≤3.5/>3.5 g/dl)", "1.378(0.834-2.277)", "0.211", "", "—", "—"], ["Creatinine (<1.1/≥1.1 mg/dl)", "0.739(0.455-1.199)", "0.221", "", "—", "—"], ["AFP a (≤300/>300 ng/ml)", "0.900(0.513-1.582)", "0.715", "", "—", "—"], ["Platelet (≤300/>300×109/L)", "0.753(0.466-1.216)", "0.246", "", "—", "—"], ["Race (Asian/White)", "0.760(0.638-0.904)", "0.002*", "", "0.766(0.630-0.930)", "0.007*"], ["BMI b (≥25<25)", "1.028(0.650-1.626)", "0.905", "", "—", "—"], ["Family history (yes/no)", "1.800(1.152-2.812)", "0.010*", "", "1.271(0.778-2.077)", "0.339"], ["ECOG c", "1.406(0.956-2.066)", "0.083", "", "—", "—"], ["Histological grade (G3-4/G1-2)", "1.247(0.802-1.938)", "0.327", "", "—", "—"]], "row_count": 18, "column_count": 6, "numeric_cells": 50, "header_rows": 0, "locator": "section[5]/table-wrap[1]#t1"}}, {"id": "asset:table:pmid:30243023:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f3a06cd1a17da4f7402be04faabc40c0ba81c9016afc31a3c1db93afec4c48a6", "bytes": 1600, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[2]#t2", "version": null, "note": "Univariate/multivariate Cox regression analysis of clinicopathologic factors associated with DFS in TCGA cohort.", "structure": {"pmcid": "PMC6188480", "section_index": 5, "section_title": "Validation and development of 12 HCC-specific gene signature for prognosis", "row_count": 18, "column_count": 6}, "table": {"label": "Table 2", "caption": "Univariate/multivariate Cox regression analysis of clinicopathologic factors associated with DFS in TCGA cohort.", "rows": [["Variables", "Univariate analysis", "", "Multivariate analysis"], ["HR (95% CI)", "P value", "", "HR (95% CI)", "P value"], ["Risk score (> 8.9/≤ 8.9)", "1.841(1.358-2.494)", "<0.001*", "", "1.483(1.038-2.117)", "0.030*"], ["TNM stage (I/II/III/IV)", "1.727(1.441-2.070)", "<0.001*", "", "1.568(1.274-1.929)", "<0.001*"], ["Hepatitis (HBV/HCV/neither)", "0.943(0.760-1.170)", "0.592", "", "—", "—"], ["Alcohol consumption (yes/no)", "1.061(0.767-1.468)", "0.720", "", "—", "—"], ["Gender (female/male)", "0.982(0.711-1.355)", "0.911", "", "—", "—"], ["Age (> 50/≤ 50)", "1.015(0.693-1.487)", "0.940", "", "—", "—"], ["Cirrhosis (yes/no)", "1.271(0.861-1.877)", "0.228", "", "—", "—"], ["Albumin (≤ 3.5/> 3.5 g/dl)", "1.033(0.702-1.519)", "0.870", "", "—", "—"], ["Creatinine (< 1.1/≥ 1.1 mg/dl)", "0.739(0.511-1.069)", "0.109", "", "—", "—"], ["AFP a (≤ 300/> 300 ng/ml)", "1.035(0.681-1.573)", "0.873", "", "—", "—"], ["Platelet (≤ 300/> 300×109/L)", "1.415(0.976-2.052)", "0.067", "", "—", "—"], ["Race (Asian/White)", "0.787(0.575-1.078)", "0.136", "", "—", "—"], ["BMI b (≥ 25/< 25 kg/m2)", "0.882(0.643-1.211)", "0.437", "", "—", "—"], ["Family history (yes/no)", "0.920(0.655-1.292)", "0.630", "", "—", "—"], ["ECOG c", "1.697(1.406-2.049)", "<0.001*", "", "1.389(1.138-1.695)", "0.001*"], ["Histological grade (G3-4/G1-2)", "1.186(0.867-1.621)", "0.286", "", "—", "—"]], "row_count": 18, "column_count": 6, "numeric_cells": 48, "header_rows": 0, "locator": "section[5]/table-wrap[2]#t2"}}, {"id": "asset:table:pmid:30243023:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7b80a4736802aaf63f78d8f52c516b3884c12520360f1b470625b4198aa3127c", "bytes": 4041, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[3]#t3", "version": null, "note": "Stratified analysis of overall and disease-free survival in TCGA samples.", "structure": {"pmcid": "PMC6188480", "section_index": 5, "section_title": "Validation and development of 12 HCC-specific gene signature for prognosis", "row_count": 50, "column_count": 8}, "table": {"label": "Table 3", "caption": "Stratified analysis of overall and disease-free survival in TCGA samples.", "rows": [["Characteristics", "Overall survival", "", "Disease-free survival"], ["High-risk / low-risk", "HR (95% CI)", "P value", "", "High-risk / low-risk", "HR (95% CI)", "P value"], ["Overall", "154/173", "1.905 (1.248-2.910)", "0.0023*", "", "164/170", "1.811 (1.329-2.466)", "<0.0001*"], ["TNM stage", "", "", "", "", "", "", ""], ["Stage I", "68/94", "2.502 (1.295-4.835)", "0.0049*", "", "63/95", "1.643 (0.9616-2.806)", "0.0509"], ["Stage II", "36/38", "1.383 (0.5167-3.700)", "0.5161", "", "39/37", "1.098 (0.5908-2.041)", "0.7632"], ["Stage III", "38/26", "2.263 (0.9245-5.539)", "0.0524", "", "49/25", "1.714 (0.9881-2.972)", "0.0592"], ["Hepatitis", "", "", "", "", "", "", ""], ["HBV", "44/50", "3.622 (1.398-9.384)", "0.015*", "", "44/48", "1.736 (0.9153-3.294)", "0.0873"], ["HCV", "25/29", "2.661 (0.8091-8.750)", "0.0644", "", "23/28", "1.263 (0.5953-2.682)", "0.5234"], ["Non-hepatitis", "81/84", "1.643 (0.9681-2.790)", "0.0539", "", "90/84", "2.157 (1.421-3.276)", "0.0002*"], ["Alcohol consumption", "", "", "", "", "", "", ""], ["Yes", "40/54", "2.235 (0.8735-5.719)", "0.0464*", "", "49/58", "3.069 (1.736-5.426)", "<0.0001*"], ["No", "110/109", "0.807 (1.107-2.951)", "0.0188*", "", "108/102", "1.429 (0.9693-2.105)", "0.0691"], ["Gender", "", "", "", "", "", "", ""], ["Male", "94/123", "2.192 (1.243-3.863)", "0.0041*", "", "103/124", "1.920 (1.304-2.826)", "0.0003*"], ["Female", "60/50", "1.420 (0.7451-2.704)", "0.2847", "", "61/46", "1.711 (1.008-2.903)", "0.048*"], ["Age", "", "", "", "", "", "", ""], ["≤ 50", "32/32", "1.553 (0.4715-5.112)", "0.4636", "", "38/30", "1.765 (0.8905-2.497)", "0.0972"], ["> 50", "122/141", "1.828 (1.165-2.868)", "0.0075*", "", "126/140", "1.808 (1.278-2.558)", "0.0004*"], ["Cirrhosis", "", "", "", "", "", "", ""], ["Yes", "34/42", "3.445 (1.244-9.539)", "0.0237*", "", "33/42", "0.9595 (0.522-1.764)", "0.8938"], ["No", "51/77", "1.323 (0.7002-2.500)", "0.3701", "", "52/74", "1.866 (1.114-3.125)", "0.0114*"], ["Albumin (g/dl)", "", "", "", "", "", "", ""], ["≤ 3.5", "44/38", "2.379 (1.030-5.495)", "0.061", "", "41/36", "1.203 (0.6193-2.337)", "0.5811"], ["> 3.5", "87/117", "1.911 (1.102-3.312)", "0.0139*", "", "82/116", "1.784 (1.183-2.691)", "0.0028*"], ["Creatinine(mg/dl)", "", "", "", "", "", "", ""], ["< 1.1", "87/108", "1.888 (1.102-3.234)", "0.0171*", "", "81/105", "1.665 (1.097-2.529)", "0.0113*"], ["≥ 1.1", "47/48", "2.148 (0.9684-4.765)", "0.0507", "", "44/45", "1.428 (0.7646-2.668)", "0.2451"], ["Alpha-fetoprotein(ng/ml)", "", "", "", "", "", "", ""], ["≤ 300", "79/125", "2.379 (1.334-4.243)", "0.0011*", "", "76/121", "1.770 (1.147-2.731)", "0.0044*"], ["> 300", "45/18", "2.148 (0.7583-6.082)", "0.2203", "", "41/17", "1.425 (0.665-3.054)", "0.3896"], ["Platelet(×109/L)", "", "", "", "", "", "", ""], ["≤ 300", "101/120", "2.421 (1.413-4.147)", "0.0013*", "", "95/119", "1.527 (1.016-2.295)", "0.0337*"], ["> 300", "34/38", "1.338 (0.5988-2.988)", "0.4481", "", "31/34", "1.772 (0.9258-3.391)", "0.0671"], ["Race", "", "", "", "", "", "", ""], ["Asian", "65/63", "4.354 (1.719-11.03)", "0.0041*", "", "83/65", "2.046 (1.270-3.297)", "0.0034*"], ["White", "76/95", "1.612 (0.9556-2.720)", "0.0623", "", "69/91", "1.901 (1.234-2.928)", "0.0015*"], ["BMIa", "", "", "", "", "", "", ""], ["< 25", "78/71", "2.331 (1.201-4.523)", "0.0175*", "", "93/71", "1.472 (0.9494-2.281)", "0.0855"], ["≥ 25", "62/91", "1.858 (0.9573-3.608)", "0.0454*", "", "56/87", "2.549 (1.546-4.204)", "<0.0001*"], ["Family history", "", "", "", "", "", "", ""], ["Yes", "52/57", "1.723 (0.9518-3.118)", "0.0669", "", "85/91", "1.543 (0.8052-2.957)", "0.1744"], ["No", "48/52", "1.882 (1.073-3.301)", "0.0214*", "", "101/90", "1.639 (1.099-2.446)", "0.0135*"], ["ECOGb", "", "", "", "", "", "", ""], ["=0", "63/95", "2.958 (1.476-5.931)", "0.002*", "", "59/93", "1.463 (0.889-2.408)", "0.1159"], [">0", "47/52", "1.454 (0.6708-3.150)", "0.3143", "", "62/52", "2.165 (1.353-3.463)", "0.001*"], ["Histological grade", "", "", "", "", "", "", ""], ["G1/2", "73/127", "1.445 (0.805-2.596)", "0.1908", "", "82/126", "1.936 (1.256-2.983)", "0.0008*"], ["G3/4", "77/45", "3.357 (1.698-6.636)", "0.0042*", "", "78/43", "1.684 (1.033-2.747)", "0.0457*"]], "row_count": 50, "column_count": 8, "numeric_cells": 217, "header_rows": 0, "locator": "section[5]/table-wrap[3]#t3"}}], "gaps": ["asset:data:geo:GSE14323 not downloaded", "asset:data:geo:GSE14323 licence not read", "asset:data:geo:GSE14520 not downloaded", "asset:data:geo:GSE14520 licence not read", "asset:data:geo:GSE15765 not downloaded", "asset:data:geo:GSE15765 licence not read", "asset:data:geo:GSE28691 not downloaded", "asset:data:geo:GSE28691 licence not read", "asset:data:geo:GSE5851 not downloaded", "asset:data:geo:GSE5851 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "False discovery rate (FDR)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "False discovery rate (FDR) was applied to compare the expression of genes between tumor and non-tumor samples."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (False discovery rate (FDR)), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["GSE5851", "GSE28691", "GSE15765", "GSE14323", "GSE14520"], "resolved_accessions": ["GSE5851", "GSE28691", "GSE15765", "GSE14323", "GSE14520"], "statements": ["We selected 75 CRCLM samples from GSE5851 (61) and GSE28691 (14), 70 HCC samples and 13 ICC samples from GSE15765 and 19 normal liver tissue samples from GSE14323 for integrated normalization and analysis."], "basis": "The paper names GSE5851, GSE28691, GSE15765, GSE14323, GSE14520 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:30243023", "data:geo:GSE14323", "asset:table:pmid:30243023:1", "asset:table:pmid:30243023:2", "asset:table:pmid:30243023:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE14323"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:12:22Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 35905, "completion_tokens": 1947, "cached_tokens": 648}}, "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:30243023", "type": "paper", "label": "pmid:30243023"}, {"id": "source:pmid:30243023", "type": "manuscript", "label": "PMID 30243023 full text"}, {"id": "data:geo:GSE14323", "type": "dataset", "label": "GEO GSE14323"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30243023", "type": "paper", "label": "pmid:30243023"}, {"id": "source:pmid:30243023", "type": "manuscript", "label": "PMID 30243023 full text"}, {"id": "data:geo:GSE14323", "type": "dataset", "label": "GEO GSE14323"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30243023", "type": "extraction", "used": ["source:pmid:30243023"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE14323", "type": "accession_resolution", "used": ["data:geo:GSE14323"], "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:30243023", "parent_hash": "sha256:71f2940b54952005b9345476583297164198a7218692723b777f40bf64723541", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE14323 licence not read", "asset:data:geo:GSE14323 not downloaded", "asset:data:geo:GSE14520 licence not read", "asset:data:geo:GSE14520 not downloaded", "asset:data:geo:GSE15765 licence not read", "asset:data:geo:GSE15765 not downloaded", "asset:data:geo:GSE28691 licence not read", "asset:data:geo:GSE28691 not downloaded", "asset:data:geo:GSE5851 licence not read", "asset:data:geo:GSE5851 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"]}