Transcription Factor Profiling to Predict Recurrence-Free Survival in Breast Cancer: Development and Validation of a Nomogram to Optimize Clinical Management.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32391054", "kind": "science-record", "revision": 6, "content_hash": "sha256:a3c7077ae6b1be378e8a10573a63634dae3fa8c9ebad5caf4a3cba15e0cf34f4", "created_at": "2026-11-01T15:41:01Z", "updated_at": "2026-11-01T21:23:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcription Factor Profiling to Predict Recurrence-Free Survival in Breast Cancer: Development and Validation of a Nomogram to Optimize Clinical Management.", "doi": "10.3389/fgene.2020.00333", "pmid": "32391054", "authors": ["Hengyu Chen", "Xianxiong Ma", "Ming Yang", "Mengyi Wang", "Lei Li", "Tao Huang"], "journal": "Frontiers in genetics", "year": 2020, "abstract": "Breast cancer (BC) is the most frequently diagnosed cancer and the leading cause of cancer-related death in young women. Several prognostic and predictive transcription factor (TF) markers have been reported for BC; however, they are inconsistent due to small datasets, the heterogeneity of BC, and variation in data pre-processing approaches. This study aimed to identify an effective predictive TF signature for the prognosis of patients with BC. We analyzed the TF data of 868 patients with BC in The Cancer Genome Atlas (TCGA) database to investigate TF biomarkers relevant to recurrence-free survival (RFS). These patients were separated into training and internal validation datasets, with GSE2034 and GSE42568 used as external validation sets. A nine-TF signature was identified as crucially related to the RFS of patients with BC by univariate Cox proportional hazard analysis, least absolute shrinkage and selection operator (LASSO) Cox regression analysis, and multivariate Cox proportional hazard analysis in the training dataset. Kaplan-Meier analysis revealed that the nine-TF signature could significantly distinguish high- and low-risk patients in both the internal validation dataset and the two external validation sets. Receiver operating characteristic (ROC) analysis further verified that the nine-TF signature showed a good performance for predicting the RFS of patients with BC. In addition, we developed a nomogram based on risk score and lymph node status, with C-index, ROC, and calibration plot analysis, suggesting that it displays good performance and clinical value. In summary, we used integrated bioinformatics approaches to identify an effective predictive nine-TF signature which may be a potential biomarker for BC prognosis.", "claims": [{"id": "claim-data-access", "statement": "All data generated or analyzed during the present study are included in this published article or are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32391054", "locator": "sections[15] \"Data Availability Statement\" paragraph 2", "quote": "All data generated or analyzed during the present study are included in this published article or are available from the corresponding author on reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:32391054"], "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:GSE2034"], "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:GSE2034"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32391054", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2020.00333", "sha256": "sha256:50faf91114520e331b30f58a238d79a95ade78a8cd43dba7998a2316818961ff", "bytes": 30876, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2020.00333", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7193038", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE2034", "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=GSE2034", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE2034", "version": null, "note": "All data generated or analyzed during the present study are included in this published article or are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during the present study are included in this published article or are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM36777", "GSM36778", "GSM36779", "GSM36780", "GSM36781", "GSM36782", "GSM36783", "GSM36784", "GSM36785", "GSM36786", "GSM36787", "GSM36788", "GSM36789", "GSM36790", "GSM36791", "GSM36792", "GSM36793", "GSM36794", "GSM36795", "GSM36796", "GSM36797", "GSM36798", "GSM36799", "GSM36800", "GSM36801", "GSM36802", "GSM36803", "GSM36804", "GSM36805", "GSM36806", "GSM36807", "GSM36808", "GSM36809", "GSM36810", "GSM36811", "GSM36812", "GSM36813", "GSM36814", "GSM36815", "GSM36816", "GSM36817", "GSM36818", "GSM36819", "GSM36820", "GSM36821", "GSM36822", "GSM36823", "GSM36824", "GSM36825", "GSM36826", "GSM36827", "GSM36828", "GSM36829", "GSM36830", "GSM36831", "GSM36832", "GSM36833", "GSM36834", "GSM36835", "GSM36836", "GSM36837", "GSM36838", "GSM36839", "GSM36840", "GSM36841", "GSM36842", "GSM36843", "GSM36844", "GSM36845", "GSM36846", "GSM36847", "GSM36848", "GSM36849", "GSM36850", "GSM36851", "GSM36852", "GSM36853", "GSM36854", "GSM36855", "GSM36856", "GSM36857", "GSM36858", "GSM36859", "GSM36860", "GSM36861", "GSM36862", "GSM36863", "GSM36864", "GSM36865", "GSM36866", "GSM36867", "GSM36868", "GSM36869", "GSM36870", "GSM36871", "GSM36872", "GSM36873", "GSM36874", "GSM36875", "GSM36876", "GSM36877", "GSM36878", "GSM36879", "GSM36880", "GSM36881", "GSM36882", "GSM36883", "GSM36884", "GSM36885", "GSM36886", "GSM36887", "GSM36888", "GSM36889", "GSM36890", "GSM36891", "GSM36892", "GSM36893", "GSM36894", "GSM36895", "GSM36896", "GSM36897", "GSM36898", "GSM36899", "GSM36900", "GSM36901", "GSM36902", "GSM36903", "GSM36904", "GSM36905", "GSM36906", "GSM36907", "GSM36908", "GSM36909", "GSM36910", "GSM36911", "GSM36912", "GSM36913", "GSM36914", "GSM36915", "GSM36916", "GSM36917", "GSM36918", "GSM36919", "GSM36920", "GSM36921", "GSM36922", "GSM36923", "GSM36924", "GSM36925", "GSM36926", "GSM36927", "GSM36928", "GSM36929", "GSM36930", "GSM36931", "GSM36932", "GSM36933", "GSM36934", "GSM36935", "GSM36936", "GSM36937", "GSM36938", "GSM36939", "GSM36940", "GSM36941", "GSM36942", "GSM36943", "GSM36944", "GSM36945", "GSM36946", "GSM36947", "GSM36948", "GSM36949", "GSM36950", "GSM36951", "GSM36952", "GSM36953", "GSM36954", "GSM36955", "GSM36956", "GSM36957", "GSM36958", "GSM36959", "GSM36960", "GSM36961", "GSM36962", "GSM36963", "GSM36964", "GSM36965", "GSM36966", "GSM36967", "GSM36968", "GSM36969", "GSM36970", "GSM36971", "GSM36972", "GSM36973", "GSM36974", "GSM36975", "GSM36976", "GSM36977", "GSM36978", "GSM36979", "GSM36980", "GSM36981", "GSM36982", "GSM36983", "GSM36984", "GSM36985", "GSM36986", "GSM36987", "GSM36988", "GSM36989", "GSM36990", "GSM36991", "GSM36992", "GSM36993", "GSM36994", "GSM36995", "GSM36996", "GSM36997", "GSM36998", "GSM36999", "GSM37000", "GSM37001", "GSM37002", "GSM37003", "GSM37004", "GSM37005", "GSM37006", "GSM37007", "GSM37008", "GSM37009", "GSM37010", "GSM37011", "GSM37012", "GSM37013", "GSM37014", "GSM37015", "GSM37016", "GSM37017", "GSM37018", "GSM37019", "GSM37020", "GSM37021", "GSM37022", "GSM37023", "GSM37024", "GSM37025", "GSM37026", "GSM37027", "GSM37028", "GSM37029", "GSM37030", "GSM37031", "GSM37032", "GSM37033", "GSM37034", "GSM37035", "GSM37036", "GSM37037", "GSM37038", "GSM37039", "GSM37040", "GSM37041", "GSM37042", "GSM37043", "GSM37044", "GSM37045", "GSM37046", "GSM37047", "GSM37048", "GSM37049", "GSM37050", "GSM37051", "GSM37052", "GSM37053", "GSM37054", "GSM37055", "GSM37056", "GSM37057", "GSM37058", "GSM37059", "GSM37060", "GSM37061", "GSM37062"], "sample_count": 286, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Breast cancer relapse free survival", "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:GSE42568", "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=GSE42568", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE42568", "version": null, "note": "All data generated or analyzed during the present study are included in this published article or are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during the present study are included in this published article or are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1045191", "GSM1045192", "GSM1045193", "GSM1045194", "GSM1045195", "GSM1045196", "GSM1045197", "GSM1045198", "GSM1045199", "GSM1045200", "GSM1045201", "GSM1045202", "GSM1045203", "GSM1045204", "GSM1045205", "GSM1045206", "GSM1045207", "GSM1045208", "GSM1045209", "GSM1045210", "GSM1045211", "GSM1045212", "GSM1045213", "GSM1045214", "GSM1045215", "GSM1045216", "GSM1045217", "GSM1045218", "GSM1045219", "GSM1045220", "GSM1045221", "GSM1045222", "GSM1045223", "GSM1045224", "GSM1045225", "GSM1045226", "GSM1045227", "GSM1045228", "GSM1045229", "GSM1045230", "GSM1045231", "GSM1045232", "GSM1045233", "GSM1045234", "GSM1045235", "GSM1045236", "GSM1045237", "GSM1045238", "GSM1045239", "GSM1045240", "GSM1045241", "GSM1045242", "GSM1045243", "GSM1045244", "GSM1045245", "GSM1045246", "GSM1045247", "GSM1045248", "GSM1045249", "GSM1045250", "GSM1045251", "GSM1045252", "GSM1045253", "GSM1045254", "GSM1045255", "GSM1045256", "GSM1045257", "GSM1045258", "GSM1045259", "GSM1045260", "GSM1045261", "GSM1045262", "GSM1045263", "GSM1045264", "GSM1045265", "GSM1045266", "GSM1045267", "GSM1045268", "GSM1045269", "GSM1045270", "GSM1045271", "GSM1045272", "GSM1045273", "GSM1045274", "GSM1045275", "GSM1045276", "GSM1045277", "GSM1045278", "GSM1045279", "GSM1045280", "GSM1045281", "GSM1045282", "GSM1045283", "GSM1045284", "GSM1045285", "GSM1045286", "GSM1045287", "GSM1045288", "GSM1045289", "GSM1045290", "GSM1045291", "GSM1045292", "GSM1045293", "GSM1045294", "GSM1045295", "GSM1045296", "GSM1045297", "GSM1045298", "GSM1045299", "GSM1045300", "GSM1045301", "GSM1045302", "GSM1045303", "GSM1045304", "GSM1045305", "GSM1045306", "GSM1045307", "GSM1045308", "GSM1045309", "GSM1045310", "GSM1045311"], "sample_count": 121, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Breast Cancer Gene Expression Analysis", "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:32391054:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f0af7edd52725f9aa11f7d0b3eb7052d50f066600839147c5f136cc69c12f3e4", "bytes": 3065, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#T1", "version": null, "note": "Clinical characteristics of patients with breast cancer who were included in the study.", "structure": {"pmcid": "PMC7193038", "section_index": 8, "section_title": "Clinical Characteristics of the Study Population", "row_count": 54, "column_count": 6}, "table": {"label": "TABLE 1", "caption": "Clinical characteristics of patients with breast cancer who were included in the study.", "rows": [["Characteristics", "Total (n = 868)", "Training dataset (n = 608)", "Internal validation dataset (n = 260)", "GSE2034 (n = 286)", "GSE42568 (n = 104)"], ["Sex", "", "", "", "", ""], ["Female", "857 (98.73)", "600 (98.68)", "257 (98.85)", "", ""], ["Male", "11 (1.27)", "8 (1.32)", "3 (1.15)", "", ""], ["Age", "", "", "", "", ""], ["≤55", "395 (45.51)", "272 (44.74)", "123 (47.31)", "", "46 (44.2)"], [">55", "473 (54.49)", "336 (55.26)", "137 (52.69)", "", "58 (55.8)"], ["Tumor", "", "", "", "", ""], ["T1", "242 (27.9)", "159 (26.2)", "83 (31.9)", "", ""], ["T2", "528 (60.8)", "379 (62.3)", "149 (57.3)", "", ""], ["T3", "63 (7.2)", "46 (7.6)", "17 (6.5)", "", ""], ["T4", "33 (3.8)", "23 (3.8)", "10 (3.8)", "", ""], ["TX", "2 (0.23)", "1 (0.16)", "1 (0.38)", "", ""], ["Lymph node status", "", "", "", "", ""], ["N0", "398 (45.9)", "274 (45.1)", "124 (47.7)", "", ""], ["N1", "318 (36.6)", "225 (37.0)", "93 (35.8)", "", ""], ["N2", "100 (11.5)", "70 (11.5)", "30 (11.5)", "", ""], ["N3", "40 (4.6)", "31 (5.1)", "9 (3.5)", "", ""], ["NX", "12 (1.38)", "8 (1.32)", "4 (1.54)", "", ""], ["Metastasis", "", "", "", "", ""], ["M0", "753 (86.75)", "522 (85.86)", "231 (88.85)", "", ""], ["M1", "16 (1.84)", "14 (2.3)", "2 (0.77)", "", ""], ["MX", "92 (10.6)", "66 (10.86)", "26 (10)", "", ""], ["TNM stage", "", "", "", "", ""], ["Stage I", "157 (18.1)", "102 (16.8)", "55 (21.2)", "", ""], ["Stage II", "514 (59.2)", "361 (59.4)", "153 (58.8)", "", ""], ["Stage III", "167 (19.2)", "122 (20.1)", "45 (17.3)", "", ""], ["Stage IV", "14 (1.61)", "13 (2.14)", "1 (0.38)", "", ""], ["Indeterminate", "16 (1.8)", "10 (1.6)", "6 (2.3)", "", ""], ["Site", "", "", "", "", ""], ["Left", "462 (53.2)", "321 (52.8)", "141 (54.2)", "", ""], ["Right", "406 (46.8)", "287 (47.2)", "119 (45.8)", "", ""], ["Estrogen receptor", "", "", "", "", ""], ["Positive", "600 (69.12)", "432 (71.1)", "168 (64.6)", "209 (73.1)", "67 (64.4)"], ["Negative", "223 (25.69)", "147 (24.2)", "76 (29.2)", "77 (26.9)", "34 (32.7)"], ["Indeterminate", "45 (5.2)", "29 (4.8)", "16 (6.2)", "", "3 (2.9)"], ["Progesterone receptor", "", "", "", "", ""], ["Positive", "515 (59.3)", "369 (60.7)", "146 (56.2)", "", ""], ["Negative", "305 (35.1)", "207 (34.0)", "98 (37.7)", "", ""], ["Indeterminate", "48 (5.5)", "32 (5.3)", "16 (6.2)", "", ""], ["Her2 receptor", "", "", "", "", ""], ["Positive", "139 (16.0)", "106 (17.4)", "33 (12.7)", "", ""], ["Negative", "440 (50.7)", "304 (50.0)", "136 (52.3)", "", ""], ["Indeterminate", "289 (33.3)", "198 (32.6)", "91 (35)", "", ""], ["Margin status", "", "", "", "", ""], ["Positive", "47 (5.41)", "33 (5.43)", "14 (5.38)", "", ""], ["Negative", "732 (84.33)", "513 (84.38)", "219 (84.23)", "", ""], ["Indeterminate", "89 (10.3)", "62 (10.2)", "27 (10.4)", "", ""], ["Race", "", "", "", "", ""], ["American Indian or Alaska Native", "1 (0.12)", "1 (0.16)", "", "", ""], ["Asian", "46 (5.3)", "32 (5.26)", "14 (5.38)", "", ""], ["Black or African American", "155 (17.86)", "115 (18.91)", "40 (15.38)", "", ""], ["White", "594 (68.43)", "408 (67.11)", "186 (71.54)", "", ""], ["Not available", "72 (8.29)", "52 (8.55)", "20 (7.69)", "", ""]], "row_count": 54, "column_count": 6, "numeric_cells": 136, "header_rows": 1, "locator": "section[8]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:32391054:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:43bcd514e568cfc2cbceb1a89d6bb2a2bd49cd2b1922b76b175647923d750f43", "bytes": 1894, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#T2", "version": null, "note": "Univariate Cox regression analysis and multivariate Cox regression analysis outcomes based on methylation risk score and other clinical factors.", "structure": {"pmcid": "PMC7193038", "section_index": 13, "section_title": "Nomogram Development and Assessment", "row_count": 13, "column_count": 9}, "table": {"label": "TABLE 2", "caption": "Univariate Cox regression analysis and multivariate Cox regression analysis outcomes based on methylation risk score and other clinical factors.", "rows": [["", "Univariate Cox regression analysis", "Multivariate Cox regression analysis"], ["Characteristics", "HR", "HR.95L", "HR.95H", "p value", "HR", "HR.95L", "HR.95H", "p value"], ["Score", "2.738045421", "2.048628528", "3.659469066", "1.01E-11", "2.510661624", "1.788829617", "3.523768687", "1.02E-07"], ["Estrogen receptor status", "0.692324993", "0.342239438", "1.400522099", "0.306355543", "0.768993041", "0.260500851", "2.270051305", "0.634356191"], ["Progesterone receptor status", "0.592458976", "0.30230991", "1.161085454", "0.127286775", "0.981504947", "0.33480194", "2.877378671", "0.972862011"], ["Her2 receptor status", "1.257944488", "0.823912985", "1.9206207", "0.287844565", "1.373910032", "0.865382257", "2.181265863", "0.178008111"], ["Tumor", "1.754711187", "0.617255141", "4.988231197", "0.291488237", "1.101502581", "0.3254944", "3.727584669", "0.87648392"], ["Lymph node status", "2.17751336", "1.49200771", "3.177975825", "5.48E-05", "1.651534043", "1.069601814", "2.550074858", "0.023602411"], ["Metastasis status", "2.520159824", "0.343448624", "18.49244717", "0.363359385", "1.858617241", "0.226521566", "15.25001838", "0.563807742"], ["Margin status", "0.7974526", "0.396241415", "1.604907073", "0.525907749", "0.634209273", "0.307262431", "1.309048428", "0.218093787"], ["Ethnicity", "0.634959689", "0.086536008", "4.659029397", "0.655117076", "1.014927373", "0.132510023", "7.773582306", "0.988619118"], ["Age", "0.97574987", "0.948136617", "1.004167323", "0.093730595", "0.979959839", "0.95094581", "1.009859108", "0.186780098"], ["Anatomic neoplasm subdivision", "1.039911088", "0.843603069", "1.281900351", "0.713889548", "0.97189382", "0.782429155", "1.207237219", "0.796654191"]], "row_count": 13, "column_count": 9, "numeric_cells": 92, "header_rows": 2, "locator": "section[13]/table-wrap[1]#T2"}}], "gaps": ["asset:data:geo:GSE2034 not downloaded", "asset:data:geo:GSE2034 licence not read", "asset:data:geo:GSE42568 not downloaded", "asset:data:geo:GSE42568 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "reordered", "quote": "“Kaplan–Meier (KM) and log-rank methods were used to compare the survival rates of the groups using the R “survival” package (Moreno-Betancur et al., 2017).”"}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"id": "method-3", "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": 0.7, "band": "medium", "quote": "Cox regression"}}], "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": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "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": ["GSE2034", "GSE42568"], "resolved_accessions": ["GSE2034", "GSE42568"], "statements": ["All data generated or analyzed during the present study are included in this published article or are available from the corresponding author on reasonable request."], "basis": "The paper names GSE2034, GSE42568 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": ["logrank_test"], "assets": ["source:pmid:32391054", "data:geo:GSE2034", "asset:table:pmid:32391054:1", "asset:table:pmid:32391054:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE2034"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:19:48Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 22670, "completion_tokens": 1815, "cached_tokens": 784}}, "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:32391054", "type": "paper", "label": "pmid:32391054"}, {"id": "source:pmid:32391054", "type": "manuscript", "label": "PMID 32391054 full text"}, {"id": "data:geo:GSE2034", "type": "dataset", "label": "GEO GSE2034"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32391054", "type": "paper", "label": "pmid:32391054"}, {"id": "source:pmid:32391054", "type": "manuscript", "label": "PMID 32391054 full text"}, {"id": "data:geo:GSE2034", "type": "dataset", "label": "GEO GSE2034"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32391054", "type": "extraction", "used": ["source:pmid:32391054"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE2034", "type": "accession_resolution", "used": ["data:geo:GSE2034"], "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:32391054", "parent_hash": "sha256:a4884005fbfa049edc012a4cca06df70f1e38364cd6617b631f8834e7d16cdee", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE2034 licence not read", "asset:data:geo:GSE2034 not downloaded", "asset:data:geo:GSE42568 licence not read", "asset:data:geo:GSE42568 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": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["“Kaplan–Meier (KM) and log-rank methods were used to compare the survival rates of the groups using the R “survival” package (Moreno-Betancur et al., 2017).”"], "order_basis": "analysis_only", "id": "assay:1"}]}