Identification and validation of potential prognostic gene biomarkers for predicting survival in patients with acute myeloid leukemia.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29138577", "kind": "science-record", "revision": 7, "content_hash": "sha256:17969565907a450d1f5b4abe99ad3783b19fa049e3da9b907c1d104d65a9fd75", "created_at": "2026-11-01T15:40:29Z", "updated_at": "2026-11-01T21:21:09Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and validation of potential prognostic gene biomarkers for predicting survival in patients with acute myeloid leukemia.", "doi": "10.2147/OTT.S147717", "pmid": "29138577", "authors": ["Rui Huang", "Xiwen Liao", "Qiaochuan Li"], "journal": "OncoTargets and therapy", "year": 2017, "abstract": "BACKGROUND: Molecular analysis is a promising source of clinically useful prognostic biomarkers. The aim of this investigation was to identify prognostic biomarkers for patients with acute myeloid leukemia (AML) by using the gene expression profile dataset from public database.\nMETHODS: The gene expression profile dataset and corresponding overall survival (OS) information of three cohorts of AML patients from GSE12417 and The Cancer Genome Atlas AML project (TCGA-LAML) were included in the present study. Prognostic gene screening was performed by using a survival package, whereas time-dependent receiver operating characteristic (ROC) curve analysis was performed using the survivalROC package.\nRESULTS: In the three cohorts, 11 genes were identified that were significantly associated with AML OS. A linear prognostic model of the 11 genes was constructed and weighted by regression coefficient (β) from the multivariate Cox regression analyses of GSE12417 HG-U133A cohort to divide patients into high- and low-risk groups. GSE12417 HG-U133 plus 2.0 and TCGA-LAML were validation cohorts. Patients assigned to the high-risk group exhibited poor OS compared to patients in the low-risk group. The 11-gene signature is a prognostic marker of AML and demonstrates good performance for predicting 1-, 3-, and 5-year OS as evaluated by survivalROC in the three cohorts.\nCONCLUSION: Our study has identified an mRNA signature including 11 genes, which may serve as a potential prognostic marker of AML.", "claims": [{"id": "claim-method", "statement": "Univariate Cox proportional hazards regression analysis was applied to estimate survival in the study sample by using a survival package in the R platform, and the low expression group was set as the reference group.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29138577", "locator": "sections[4] \"Identification of prognostic gene markers\" paragraph 2", "quote": "Univariate Cox proportional hazards regression analysis was applied to estimate survival in the study sample by using a survival package in the R platform, and the low expression group was set as the reference group."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The bone marrow expression profile dataset of AML patients with complete survival data available was included in the present study.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29138577", "locator": "sections[3] \"Data source and preprocessing\" paragraph 2", "quote": "The bone marrow expression profile dataset of AML patients with complete survival data available was included in the present study."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study screened AML prognostic markers with univariate Cox proportional hazards regression, constructed an 11-gene linear risk score from multivariate Cox regression coefficients, and evaluated time-dependent survival prediction with survivalROC using GSE12417 and TCGA-LAML data; the high-risk group had worse overall survival in all three cohorts, with discovery-cohort HR 2.03 (95% CI 1.359–3.032) and 1-, 3-, and 5-year survival AUCs of 0.729, 0.722, and 0.703.", "kind": "quantitative", "target": {"value": 95.0, "unit": "per cent", "tolerance": null, "source": "Survival analysis demonstrated that patients with a high-risk score had an increased risk of death compared to the low-risk group (log-rank P=0.0004, HR =2.03, 95% CI =1.359–3.032, Figure 5B)."}, "evidence": [{"asset": "source:pmid:29138577", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The gene expression profile dataset and corresponding overall survival (OS) information of three cohorts of AML patients from GSE12417 and The Cancer Genome Atlas AML project (TCGA-LAML) were included in the present study."}, {"asset": "source:pmid:29138577", "locator": "sections[4] \"Identification of prognostic gene markers\" paragraph 2", "quote": "Univariate Cox proportional hazards regression analysis was applied to estimate survival in the study sample by using a survival package in the R platform, and the low expression group was set as the reference group."}, {"asset": "source:pmid:29138577", "locator": "sections[5] \"Construction and validation of the prognostic gene signature\" paragraph 2", "quote": "These prognostic gene markers from the GSE12417 HG-U133A cohort were fitted in a multivariate Cox regression model with OS as a dependent variable to measure the relative contributions for survival prediction."}, {"asset": "source:pmid:29138577", "locator": "sections[5] \"Construction and validation of the prognostic gene signature\" paragraph 2", "quote": "The time-dependent receiver operating characteristic (ROC) curve analysis was performed using the survivalROC package in the R platform to evaluate the predictive accuracy of the prognostic signature for time-dependent cancer death."}, {"asset": "source:pmid:29138577", "locator": "sections[10] \"Prognostic gene signature construction and validation\" paragraph 2", "quote": "Survival analysis demonstrated that patients with a high-risk score had an increased risk of death compared to the low-risk group (log-rank P=0.0004, HR =2.03, 95% CI =1.359–3.032, Figure 5B)."}, {"asset": "source:pmid:29138577", "locator": "sections[10] \"Prognostic gene signature construction and validation\" paragraph 2", "quote": "The prognostic signature in the GSE12417 HG-U133A cohort showed a good performance in the prediction of clinical outcome, as the area under the ROC curve (AUC) was 0.729, 0.722, and 0.703 for 1-, 3-, and 5-year survivals (Figure 5C), respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study screened AML prognostic markers with univariate Cox proportional hazards regression, constructed an 11-gene linear risk score from multivariate Cox regression coefficients, and evaluated time-dependent survival prediction with survivalROC using GSE12417 and TCGA-LAML data; the high-risk group had worse overall survival in all three cohorts, with discovery-cohort HR 2.03 (95% CI 1.359–3.032) and 1-, 3-, and 5-year survival AUCs of 0.729, 0.722, and 0.703.", "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:29138577"], "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:GSE12417"], "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:GSE12417"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29138577", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/OTT.S147717", "sha256": "sha256:6e6e482788e6dbdcbe200abbb6dd985ed5b939aeb5c17707fef36f0d5098fbd9", "bytes": 35133, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/OTT.S147717", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5679677", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE12417", "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=GSE12417", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE12417", "version": null, "note": "The bone marrow expression profile dataset of AML patients with complete survival data available was included in the present study.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The bone marrow expression profile dataset of AML patients with complete survival data available was included in the present study.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM311598", "GSM311599", "GSM311600", "GSM311601", "GSM311602", "GSM311603", "GSM311604", "GSM311605", "GSM311606", "GSM311607", "GSM311608", "GSM311609", "GSM311610", "GSM311611", "GSM311612", "GSM311613", "GSM311614", "GSM311615", "GSM311616", "GSM311617", "GSM311618", "GSM311619", "GSM311620", "GSM311621", "GSM311622", "GSM311623", "GSM311624", "GSM311625", "GSM311626", "GSM311627", "GSM311628", "GSM311629", "GSM311630", "GSM311631", "GSM311632", "GSM311633", "GSM311634", "GSM311635", "GSM311636", "GSM311637", "GSM311638", "GSM311639", "GSM311640", "GSM311641", "GSM311642", "GSM311643", "GSM311644", "GSM311645", "GSM311646", "GSM311647", "GSM311648", "GSM311649", "GSM311650", "GSM311651", "GSM311652", "GSM311653", "GSM311654", "GSM311655", "GSM311656", "GSM311657", "GSM311658", "GSM311659", "GSM311660", "GSM311661", "GSM311662", "GSM311663", "GSM311664", "GSM311665", "GSM311666", "GSM311667", "GSM311668", "GSM311669", "GSM311670", "GSM311671", "GSM311672", "GSM311673", "GSM311674", "GSM311675", "GSM311676", "GSM311677", "GSM311678", "GSM311679", "GSM311680", "GSM311681", "GSM311682", "GSM311683", "GSM311684", "GSM311685", "GSM311686", "GSM311687", "GSM311688", "GSM311689", "GSM311690", "GSM311691", "GSM311692", "GSM311693", "GSM311694", "GSM311695", "GSM311696", "GSM311697", "GSM311698", "GSM311699", "GSM311700", "GSM311701", "GSM311702", "GSM311703", "GSM311704", "GSM311705", "GSM311706", "GSM311707", "GSM311708", "GSM311709", "GSM311710", "GSM311711", "GSM311712", "GSM311713", "GSM311714", "GSM311715", "GSM311716", "GSM311717", "GSM311718", "GSM311719", "GSM311720", "GSM311721", "GSM311722", "GSM311723", "GSM311724", "GSM311725", "GSM311726", "GSM311727", "GSM311728", "GSM311729", "GSM311730", "GSM311731", "GSM311732", "GSM311733", "GSM311734", "GSM311735", "GSM311736", "GSM311737", "GSM311738", "GSM311739", "GSM311740", "GSM311741", "GSM311742", "GSM311743", "GSM311744", "GSM311745", "GSM311746", "GSM311747", "GSM311748", "GSM311749", "GSM311750", "GSM311751", "GSM311752", "GSM311753", "GSM311754", "GSM311755", "GSM311756", "GSM311757", "GSM311758", "GSM311759", "GSM311760", "GSM311761", "GSM311762", "GSM311763", "GSM311764", "GSM311765", "GSM311766", "GSM311767", "GSM311768", "GSM311769", "GSM311770", "GSM311771", "GSM311772", "GSM311773", "GSM311774", "GSM311775", "GSM311776", "GSM311777", "GSM311778", "GSM311779", "GSM311780", "GSM311781", "GSM311782", "GSM311783", "GSM311784", "GSM311785", "GSM311786", "GSM311787", "GSM311788", "GSM311789", "GSM311790", "GSM311791", "GSM311792", "GSM311793", "GSM311794", "GSM311795", "GSM311796", "GSM311797", "GSM311798", "GSM311799", "GSM311800", "GSM311801", "GSM311802", "GSM311803", "GSM311804", "GSM311805", "GSM311806", "GSM311807", "GSM311808", "GSM311809", "GSM311810", "GSM311811", "GSM311812", "GSM311813", "GSM311814", "GSM311815", "GSM311816", "GSM311817", "GSM311818", "GSM311819", "GSM311820", "GSM311821", "GSM311822", "GSM311823", "GSM311824", "GSM311825", "GSM311826", "GSM311827", "GSM311828", "GSM311829", "GSM311830", "GSM311831", "GSM311832", "GSM311833", "GSM311834", "GSM311835", "GSM311836", "GSM311837", "GSM311838", "GSM311839", "GSM311840", "GSM311841", "GSM311842", "GSM311843", "GSM311844", "GSM311845", "GSM311846", "GSM311847", "GSM311848", "GSM311849", "GSM311850", "GSM311851", "GSM311852", "GSM311853", "GSM311854", "GSM311855", "GSM311856", "GSM311857", "GSM311858", "GSM311859", "GSM311860", "GSM311861", "GSM311862", "GSM311863", "GSM311864", "GSM311865", "GSM311866", "GSM311867", "GSM311868", "GSM311869", "GSM311870", "GSM311871", "GSM311872", "GSM311873", "GSM311874", "GSM311875", "GSM311876", "GSM311877", "GSM311878", "GSM311879", "GSM311880", "GSM311881", "GSM311882", "GSM311883", "GSM311884", "GSM311885", "GSM311886", "GSM311887", "GSM311888", "GSM311889", "GSM311890", "GSM311891", "GSM311892", "GSM311893", "GSM311894", "GSM311895", "GSM311896", "GSM311897", "GSM311898", "GSM311899", "GSM311900", "GSM311901", "GSM311902", "GSM311903", "GSM311904", "GSM311905", "GSM311906", "GSM311907", "GSM311908", "GSM311909", "GSM311910", "GSM311911", "GSM311912", "GSM311913", "GSM311914", "GSM311915", "GSM311916", "GSM311917", "GSM311918", "GSM311919", "GSM311920", "GSM311921", "GSM311922", "GSM311923", "GSM316652", "GSM316653", "GSM316654", "GSM316655", "GSM316656", "GSM316657", "GSM316658", "GSM316659", "GSM316660", "GSM316661", "GSM316662", "GSM316663", "GSM316664", "GSM316665", "GSM316666", "GSM316667", "GSM316668", "GSM316669", "GSM316670", "GSM316671", "GSM316672", "GSM316673", "GSM316674", "GSM316675", "GSM316676", "GSM316677", "GSM316678", "GSM316679", "GSM316680", "GSM316681", "GSM316682", "GSM316683", "GSM316684", "GSM316685", "GSM316686", "GSM316687", "GSM316688", "GSM316689", "GSM316690", "GSM316691", "GSM316692", "GSM316693", "GSM316694", "GSM316695", "GSM316696", "GSM316697", "GSM316698", "GSM316699", "GSM316700", "GSM316701", "GSM316702", "GSM316703", "GSM316704", "GSM316705", "GSM316706", "GSM316707", "GSM316708", "GSM316709", "GSM316710", "GSM316711", "GSM316712", "GSM316713", "GSM316714", "GSM316715", "GSM316716", "GSM316717", "GSM316718", "GSM316719", "GSM316720", "GSM316721", "GSM316722", "GSM316723", "GSM316724", "GSM316725", "GSM316726", "GSM316727", "GSM316728", "GSM316729", "GSM316730"], "sample_count": 405, "group_sizes": null, "group_sizes_basis": null, "platform": "570;96;97", "taxon": "Homo sapiens", "title": "Prognostic gene signature for normal karyotype AML", "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:29138577:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:467b739d52fe85f330ee1f97728f0c2e97441bed963f1cd911f63aac1a339383", "bytes": 1747, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#t1-ott-10-5243", "version": null, "note": "Prognostic value of the 11 genes in AML patients of the three cohorts", "structure": {"pmcid": "PMC5679677", "section_index": 10, "section_title": "Prognostic gene signature construction and validation", "row_count": 13, "column_count": 8}, "table": {"label": "Table 1", "caption": "Prognostic value of the 11 genes in AML patients of the three cohorts", "rows": [["Gene symbol", "GSE12417 HG-U133A cohort", "GSE12417 HG-U133 plus 2.0 cohort", "TCGA-LAML cohort"], ["HR (95% CI)a", "Log-rankP-value", "Coefficient βb", "HR (95% CI)a", "Log-rankP-value", "HR (95% CI)a", "Log-rankP-value"], ["ACSF2", "1.803 (1.214–2.679)", "0.0031", "0.438", "1.886 (1.017–3.499)", "0.0407", "1.718 (1.119–2.639)", "0.0124"], ["CXCR6", "0.640 (0.432–0.950)", "0.0327", "−0.077", "0.505 (0.270–0.945)", "0.0294", "0.653 (0.427–0.998)", "0.0495"], ["FAM124B", "1.782 (1.199–2.648)", "0.0037", "0.295", "2.556 (1.361–4.799)", "0.0025", "1.852 (1.204–2.846)", "0.0042"], ["FRYL", "0.637 (0.430–0.944)", "0.0234", "−0.391", "0.534 (0.287–0.992)", "0.0437", "0.529 (0.345–0.813)", "0.0032"], ["GYPA", "0.580 (0.392–0.859)", "0.0059", "−0.289", "0.532 (0.288–0.983)", "0.0405", "0.611 (0.400–0.936)", "0.0225"], ["HBG1", "0.599 (0.405–0.887)", "0.0098", "−0.072", "0.429 (0.229–0.802)", "0.0064", "0.598 (0.391–0.917)", "0.0174"], ["MAGOH", "1.822 (1.226–2.709)", "0.0026", "0.387", "1.858 (1.001–3.448)", "0.0464", "1.613 (1.052–2.474)", "0.0267"], ["MDH2", "1.749 (1.178–2.596)", "0.005", "−0.106", "2.007 (1.080–3.729)", "0.0246", "1.652 (1.080–2.526)", "0.0199"], ["SLC2A5", "1.603 (1.079–2.381)", "0.0183", "0.329", "2.036 (1.093–3.792)", "0.0222", "1.905 (1.242–2.922)", "0.0026"], ["SUCLG1", "1.661 (1.121–2.463)", "0.0078", "0.221", "1.887 (1.022–3.484)", "0.0394", "2.076 (1.349–3.193)", "0.0007"], ["TMC5", "0.646 (0.436–0.955)", "0.0145", "−0.35", "0.507 (0.273–0.940)", "0.028", "0.569 (0.370–0.875)", "0.0098"]], "row_count": 13, "column_count": 8, "numeric_cells": 83, "header_rows": 2, "locator": "section[10]/table-wrap[1]#t1-ott-10-5243"}}], "gaps": ["asset:data:geo:GSE12417 not downloaded", "asset:data:geo:GSE12417 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": "Univariate Cox proportional hazards regression analysis was applied to estimate survival in the study sample by using a survival package in the R platform, and the low expression group was set as the reference group."}}, {"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": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "cox_ph", "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."}, {"id": "target-published-estimate-hazard-ratio", "claim_id": "claim-target-result", "operation": "cox_ph", "expected_value": 2.03, "unit": "hazard ratio", "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."}, {"id": "target-published-estimate-p-value", "claim_id": "claim-target-result", "operation": "cox_ph", "expected_value": 0.0004, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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": ["GSE12417"], "resolved_accessions": ["GSE12417"], "statements": ["The bone marrow expression profile dataset of AML patients with complete survival data available was included in the present study."], "basis": "The paper names GSE12417 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:29138577", "data:geo:GSE12417", "asset:table:pmid:29138577:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE12417"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:32:51Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 78697, "completion_tokens": 3764, "cached_tokens": 2088}}, "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:29138577", "type": "paper", "label": "pmid:29138577"}, {"id": "source:pmid:29138577", "type": "manuscript", "label": "PMID 29138577 full text"}, {"id": "data:geo:GSE12417", "type": "dataset", "label": "GEO GSE12417"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29138577", "type": "paper", "label": "pmid:29138577"}, {"id": "source:pmid:29138577", "type": "manuscript", "label": "PMID 29138577 full text"}, {"id": "data:geo:GSE12417", "type": "dataset", "label": "GEO GSE12417"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29138577", "type": "extraction", "used": ["source:pmid:29138577"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE12417", "type": "accession_resolution", "used": ["data:geo:GSE12417"], "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:29138577", "parent_hash": "sha256:57ecf72c58ba02fe2c682ea5ffaae151de46237ed93feeb5b549134fd221ea50", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE12417 licence not read", "asset:data:geo:GSE12417 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": ["Univariate Cox proportional hazards regression analysis was applied to estimate survival in the study sample by using a survival package in the R platform, and the low expression group was set as the reference group."], "order_basis": "analysis_only", "id": "assay:1"}]}