← All .science files
pmid:31552180
Development and External Validation of a Novel 12-Gene Signature for Prediction of Overall Survival in Muscle-Invasive Bladder Cancer.
MierXiati Abudurexiti · Huyang Xie · Zhongwei Jia · Yiping Zhu · Yao Zhu · Guohai Shi · Hailiang Zhang · Bo Dai · Fangning Wan · Yijun Shen · Dingwei Ye
Frontiers in oncology · 2019 doi:10.3389/fonc.2019.00856
Paper
complete
Experiment
complete
Data
partial
Analysis
complete
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 11 items
claims array · 2 items
[0] object · 6 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 7 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 256 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 33 items
[0] array · 4 items
[1] array · 7 items
[2] array · 7 items
[3] array · 1 item
[4] array · 7 items
[5] array · 7 items
[6] array · 1 item
[7] array · 7 items
[8] array · 7 items
[9] array · 7 items
[10] array · 1 item
[11] array · 7 items
[12] array · 7 items
[13] array · 7 items
[14] array · 7 items
[15] array · 7 items
[16] array · 7 items
[17] array · 1 item
[18] array · 7 items
[19] array · 7 items
[20] array · 7 items
[21] array · 7 items
[22] array · 7 items
[23] array · 1 item
[24] array · 7 items
[25] array · 7 items
[26] array · 7 items
[27] array · 1 item
[28] array · 7 items
[29] array · 7 items
[30] array · 7 items
[31] array · 7 items
[32] array · 7 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 71 items
[0] array · 4 items
[1] array · 4 items
[2] array · 4 items
[3] array · 4 items
[4] array · 4 items
[5] array · 4 items
[6] array · 4 items
[7] array · 4 items
[8] array · 4 items
[9] array · 4 items
[10] array · 4 items
[11] array · 4 items
[12] array · 4 items
[13] array · 4 items
[14] array · 4 items
[15] array · 4 items
[16] array · 4 items
[17] array · 4 items
[18] array · 4 items
[19] array · 4 items
[20] array · 4 items
[21] array · 4 items
[22] array · 4 items
[23] array · 4 items
[24] array · 4 items
[25] array · 4 items
[26] array · 4 items
[27] array · 4 items
[28] array · 4 items
[29] array · 4 items
[30] array · 4 items
[31] array · 4 items
[32] array · 4 items
[33] array · 4 items
[34] array · 4 items
[35] array · 4 items
[36] array · 4 items
[37] array · 4 items
[38] array · 4 items
[39] array · 4 items
[40] array · 4 items
[41] array · 4 items
[42] array · 4 items
[43] array · 4 items
[44] array · 4 items
[45] array · 4 items
[46] array · 4 items
[47] array · 4 items
[48] array · 4 items
[49] array · 4 items
[50] array · 4 items
[51] array · 4 items
[52] array · 4 items
[53] array · 4 items
[54] array · 4 items
[55] array · 4 items
[56] array · 4 items
[57] array · 4 items
[58] array · 4 items
[59] array · 4 items
[60] array · 4 items
[61] array · 4 items
[62] array · 4 items
[63] array · 4 items
[64] array · 4 items
[65] array · 4 items
[66] array · 4 items
[67] array · 4 items
[68] array · 4 items
[69] array · 4 items
[70] array · 4 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 13 items
[0] array · 3 items
[1] array · 3 items
[2] array · 3 items
[3] array · 3 items
[4] array · 3 items
[5] array · 3 items
[6] array · 3 items
[7] array · 3 items
[8] array · 3 items
[9] array · 3 items
[10] array · 3 items
[11] array · 3 items
[12] array · 3 items
[5] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 14 items
[0] array · 3 items
[1] array · 7 items
[2] array · 7 items
[3] array · 7 items
[4] array · 7 items
[5] array · 7 items
[6] array · 7 items
[7] array · 7 items
[8] array · 7 items
[9] array · 7 items
[10] array · 7 items
[11] array · 7 items
[12] array · 7 items
[13] array · 7 items
[6] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 4 items
[0] array · 4 items
[1] array · 4 items
[2] array · 4 items
[3] array · 4 items
gaps array · 2 items
analysis object · 4 fields
methods array · 2 items
[0] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 6 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 1 item
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 1 item
assets array · 7 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 6 items
assays array · 2 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
[1] object · 11 fields
required_operations array · 1 item
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31552180", "kind": "science-record", "revision": 7, "content_hash": "sha256:7e345b734141ef7537871f62174b9d0e1447f6dc0698b344670d983ad9d27001", "created_at": "2026-11-01T15:40:49Z", "updated_at": "2026-11-01T22:00:52Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Development and External Validation of a Novel 12-Gene Signature for Prediction of Overall Survival in Muscle-Invasive Bladder Cancer.", "doi": "10.3389/fonc.2019.00856", "pmid": "31552180", "authors": ["MierXiati Abudurexiti", "Huyang Xie", "Zhongwei Jia", "Yiping Zhu", "Yao Zhu", "Guohai Shi", "Hailiang Zhang", "Bo Dai", "Fangning Wan", "Yijun Shen", "Dingwei Ye"], "journal": "Frontiers in oncology", "year": 2019, "abstract": "Purpose: We aimed to develop and validate a novel gene signature from published data and improve the prediction of survival in muscle-invasive bladder cancer (MIBC). Methods: We searched the published gene signatures associated with the overall survival (OS) of MIBC and compiled all 274 genes to develop a novel gene signature. RNAseq data of TCGA (the Cancer Genome Atlas) bladder cohort were downloaded. All genes were included in a univariate Cox hazard ratio model. We then used a reduced multivariate Cox regression model, which included only genes achieving P < 0.05 in the univariate model. A total of 172 patients at Fudan University Shanghai Cancer Center (FUSCC) and 61 patients from GEO datasets were used as an external validation set. Results: A total of 327 patients in the TCGA cohort were enrolled. We identified 274 genes from eight published papers on the OS of MIBC. Using the TCGA database, we identified 12 genes that correlated with OS (P < 0.05 in both univariate and multivariate analyses). By integrating these genes with the RT-qPCR data in our validation dataset and GEO datasets, we confirmed that the power for predicting OS of the 12-gene panel (AUC of 0.741 and 0.727, respectively) was higher than just clinical data (including gender, age, T stage, grade, and N stage) alone in the TCGA and FUSCC cohort (AUC of 0.667 and 0.631, respectively). Additionally, upon combining the clinical data and 12-gene panel together, the AUC increased to 0.768, 0.757, and 0.88 in the TCGA, FUSCC and GSE13507 cohorts, respectively. Conclusions: Applying published gene signatures and TCGA data, we successfully built and externally validated a novel 12-gene signature for the survival of MIBC.\nBRIEF EXPLANATION: We systemically reviewed all published prognostic gene signatures of muscle-invasive bladder cancer (MIBC) and integrated the genes in the TCGA MIBC cohort. This new gene panel was validated in a newly established MIBC cohort in GEO and FUSCC. This method can help update the previous established panels in a new way.", "claims": [{"id": "claim-method", "statement": "For the data obtained by qRT-PCR, univariate and multivariate Cox regression models were used for the selection of genes for the predictive gene signature.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31552180", "locator": "sections[6] \"Statistical Analysis\" paragraph 2", "quote": "For the data obtained by qRT-PCR, univariate and multivariate Cox regression models were used for the selection of genes for the predictive gene signature."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All datasets generated for this study are included in the manuscript and/or the Supplementary Files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31552180", "locator": "sections[15] \"Data Availability\" paragraph 2", "quote": "All datasets generated for this study are included in the manuscript and/or the Supplementary Files."}], "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:31552180"], "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:GSE13507"], "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:GSE13507"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31552180", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2019.00856", "sha256": "sha256:0fbb39f5170de010ef58df9848b2e9fd43890f9b5c5ed90dde6d26398c981c7d", "bytes": 34063, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2019.00856", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6743371", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13507", "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=GSE13507", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13507", "version": null, "note": "All datasets generated for this study are included in the manuscript and/or the Supplementary Files.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All datasets generated for this study are included in the manuscript and/or the Supplementary Files.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM340537", "GSM340538", "GSM340539", "GSM340540", "GSM340541", "GSM340542", "GSM340543", "GSM340544", "GSM340545", "GSM340546", "GSM340547", "GSM340548", "GSM340549", "GSM340550", "GSM340551", "GSM340552", "GSM340553", "GSM340554", "GSM340555", "GSM340556", "GSM340557", "GSM340558", "GSM340559", "GSM340560", "GSM340561", "GSM340562", "GSM340563", "GSM340564", "GSM340565", "GSM340566", "GSM340567", "GSM340568", "GSM340569", "GSM340570", "GSM340571", "GSM340572", "GSM340573", "GSM340574", "GSM340575", "GSM340576", "GSM340577", "GSM340578", "GSM340579", "GSM340580", "GSM340581", "GSM340582", "GSM340583", "GSM340584", "GSM340585", "GSM340586", "GSM340587", "GSM340588", "GSM340589", "GSM340590", "GSM340591", "GSM340592", "GSM340593", "GSM340594", "GSM340595", "GSM340596", "GSM340597", "GSM340598", "GSM340599", "GSM340600", "GSM340601", "GSM340602", "GSM340603", "GSM340604", "GSM340605", "GSM340606", "GSM340607", "GSM340608", "GSM340609", "GSM340610", "GSM340611", "GSM340612", "GSM340613", "GSM340614", "GSM340615", "GSM340616", "GSM340617", "GSM340618", "GSM340619", "GSM340620", "GSM340621", "GSM340622", "GSM340623", "GSM340624", "GSM340625", "GSM340626", "GSM340627", "GSM340628", "GSM340629", "GSM340630", "GSM340631", "GSM340632", "GSM340633", "GSM340634", "GSM340635", "GSM340636", "GSM340637", "GSM340638", "GSM340639", "GSM340640", "GSM340641", "GSM340642", "GSM340643", "GSM340644", "GSM340645", "GSM340646", "GSM340647", "GSM340648", "GSM340649", "GSM340650", "GSM340651", "GSM340652", "GSM340653", "GSM340654", "GSM340655", "GSM340656", "GSM340657", "GSM340658", "GSM340659", "GSM340660", "GSM340661", "GSM340662", "GSM340663", "GSM340664", "GSM340665", "GSM340666", "GSM340667", "GSM340668", "GSM340669", "GSM340670", "GSM340671", "GSM340672", "GSM340673", "GSM340674", "GSM340675", "GSM340676", "GSM340677", "GSM340678", "GSM340679", "GSM340680", "GSM340681", "GSM340682", "GSM340683", "GSM340684", "GSM340685", "GSM340686", "GSM340687", "GSM340688", "GSM340689", "GSM340690", "GSM340691", "GSM340692", "GSM340693", "GSM340694", "GSM340695", "GSM340696", "GSM340697", "GSM340698", "GSM340699", "GSM340700", "GSM340701", "GSM340702", "GSM340703", "GSM340704", "GSM340705", "GSM340706", "GSM340707", "GSM340708", "GSM340709", "GSM340710", "GSM340711", "GSM340712", "GSM340713", "GSM340714", "GSM340715", "GSM340716", "GSM340717", "GSM340718", "GSM340719", "GSM340720", "GSM340721", "GSM340722", "GSM340723", "GSM340724", "GSM340725", "GSM340726", "GSM340727", "GSM340728", "GSM340729", "GSM340730", "GSM340731", "GSM340732", "GSM340733", "GSM340734", "GSM340735", "GSM340736", "GSM340737", "GSM340738", "GSM340739", "GSM340740", "GSM340741", "GSM340742", "GSM340743", "GSM340744", "GSM340745", "GSM340746", "GSM340747", "GSM340748", "GSM340749", "GSM340750", "GSM340751", "GSM340752", "GSM340753", "GSM340754", "GSM340755", "GSM340756", "GSM340757", "GSM340758", "GSM340759", "GSM340760", "GSM340761", "GSM340762", "GSM340763", "GSM340764", "GSM340765", "GSM340766", "GSM340767", "GSM340768", "GSM340769", "GSM340770", "GSM340771", "GSM340772", "GSM340773", "GSM340774", "GSM340775", "GSM340776", "GSM340777", "GSM340778", "GSM340779", "GSM340780", "GSM340781", "GSM340782", "GSM340783", "GSM340784", "GSM340785", "GSM340786", "GSM340787", "GSM340788", "GSM340789", "GSM340790", "GSM340791", "GSM340792"], "sample_count": 256, "group_sizes": null, "group_sizes_basis": null, "platform": "6102", "taxon": "Homo sapiens", "title": "Predective Value of Prognosis-Related Gene Expression Study in Primary Bladder Cancer", "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:31552180:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:704c3d7b7587cb36b1868123f6076630071d8f9abdb7033665b80621719b93e7", "bytes": 1461, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#T1", "version": null, "note": "Clinical characteristics of bladder cancer patients in each cohort.", "structure": {"pmcid": "PMC6743371", "section_index": 4, "section_title": "Patient Cohorts", "row_count": 33, "column_count": 7}, "table": {"label": "Table 1", "caption": "Clinical characteristics of bladder cancer patients in each cohort.", "rows": [["Variables", "TCGA cohort", "GEO cohort", "FUSCC cohort"], ["", "N = 327", "%", "N = 61", "%", "N = 172", "%"], ["Age, median (range)", "69", "38–90", "66", "38–87", "63", "31–87"], ["Gender"], ["Male", "239", "73.09", "48", "78.69", "147", "85.47"], ["Female", "88", "26.91", "13", "21.31", "25", "14.53"], ["Grade"], ["High", "313", "95.72", "42", "68.85", "163", "94.77"], ["Low", "12", "3.67", "19", "31.15", "7", "4.07"], ["Gx", "2", "0.61", "", "", "2", "1.16"], ["pT"], ["T0", "2", "0.61", "", "", "0", "0"], ["T1", "2", "0.61", "", "", "5", "2.91"], ["T2", "95", "29.05", "31", "50.82", "63", "36.63"], ["T3", "154", "47.09", "19", "31.15", "41", "23.84"], ["T4", "49", "14.98", "11", "18.03", "29", "16.86"], ["Tx", "25", "7.65", "", "", "34", "19.77"], ["N"], ["N0", "190", "58.1", "46", "75.41", "106", "61.63"], ["N1", "35", "10.7", "8", "13.11", "12", "6.98"], ["N2", "64", "19.57", "6", "9.84", "19", "11.05"], ["N3", "7", "2.14", "", "", "0", "0"], ["Nx", "31", "9.48", "1", "1.64", "35", "20.35"], ["M"], ["M0", "155", "47.4", "55", "90.16", "155", "90.12"], ["M1", "7", "2.14", "6", "9.84", "7", "4.07"], ["Mx", "165", "50.46", "", "", "10", "5.81"], ["Stage"], ["I", "2", "0.61", "", "", "5", "2.91"], ["II", "102", "31.19", "26", "42.62", "54", "31.4"], ["III", "108", "33.03", "13", "21.31", "37", "21.51"], ["IV", "111", "33.94", "6", "9.84", "52", "30.23"], ["X", "4", "1.22", "16", "26.23", "24", "13.95"]], "row_count": 33, "column_count": 7, "numeric_cells": 139, "header_rows": 2, "locator": "section[4]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:31552180:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0564dd5f75dc933c59d159c2ba0e828c012d540432656e891db26c3b63f136b0", "bytes": 3378, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#T2", "version": null, "note": "Multivariate Cox hazard ratio regression model of integrated gene list in TCGA BLCA cohort.", "structure": {"pmcid": "PMC6743371", "section_index": 9, "section_title": "Gene List Discovery Using TCGA Database", "row_count": 71, "column_count": 4}, "table": {"label": "Table 2", "caption": "Multivariate Cox hazard ratio regression model of integrated gene list in TCGA BLCA cohort.", "rows": [["Gene IDs", "OR", "95%CI", "P-value"], ["ARFGEF1", "0.953", "(0.441–2.061)", "0.902"], ["ARID4B", "0.516", "(0.246–1.081)", "0.080"], ["ATIC", "1.698", "(1.065–2.708)", "0.026"], ["BIRC5", "1.360", "(0.902–2.050)", "0.142"], ["C15orf53", "0.852", "(0.549–1.323)", "0.476"], ["C6orf62", "0.346", "(0.201–0.595)", "0.000"], ["CALR", "1.052", "(0.554–1.998)", "0.878"], ["CATSPERG", "0.868", "(0.707–1.066)", "0.176"], ["CBX7", "0.908", "(0.657–1.254)", "0.557"], ["CDA", "0.857", "(0.703–1.044)", "0.125"], ["CHD3", "1.257", "(0.734–2.155)", "0.405"], ["COL5A1", "1.258", "(0.924–1.713)", "0.145"], ["CORO1C", "1.205", "(0.635–2.289)", "0.568"], ["CPA4", "0.881", "(0.785–0.988)", "0.031"], ["CYFIP2", "1.279", "(1.011–1.618)", "0.041"], ["DNASE2B", "0.826", "(0.627–1.087)", "0.173"], ["DPP4", "0.987", "(0.845–1.153)", "0.873"], ["EGFR", "1.183", "(1.007–1.390)", "0.041"], ["EHBP1", "2.637", "(1.575–4.414)", "0.000"], ["EHF", "1.044", "(0.869–1.255)", "0.645"], ["ENDOD1", "1.126", "(0.783–1.620)", "0.522"], ["ERBB3", "1.067", "(0.805–1.415)", "0.650"], ["ERC1", "1.264", "(0.771–2.074)", "0.353"], ["ESR2", "1.043", "(0.788–1.380)", "0.771"], ["ESYT1", "1.367", "(0.799–2.388)", "0.254"], ["FADD", "1.369", "(0.956–1.961)", "0.086"], ["FN1", "0.912", "(0.688–1.208)", "0.520"], ["FUCA1", "1.402", "(0.994–1.977)", "0.054"], ["FXYD3", "0.854", "(0.693–1.053)", "0.139"], ["GPC3", "0.944", "(0.826–1.079)", "0.402"], ["GRK3", "0.752", "(0.591–0.957)", "0.021"], ["HSD17B1", "1.122", "(0.954–1.318)", "0.165"], ["LGALS1", "1.055", "(0.774–1.438)", "0.736"], ["LIMCH1", "0.839", "(0.681–1.035)", "0.101"], ["MAP2K1", "1.089", "(0.616–1.926)", "0.770"], ["MARCH7", "0.412", "(0.217–0.784)", "0.007"], ["MECOM", "0.920", "(0.676–1.250)", "0.593"], ["METTL21EP", "0.902", "(0.650–1.254)", "0.540"], ["MMP14", "0.988", "(0.663–1.472)", "0.953"], ["MMP16", "0.965", "(0.782–1.191)", "0.739"], ["MPRIP", "1.045", "(0.657–1.661)", "0.853"], ["NCAPG2", "0.688", "(0.444–1.065)", "0.094"], ["NCLN", "1.154", "(0.608–2.191)", "0.661"], ["NOL12", "0.928", "(0.552–1.648)", "0.798"], ["NOTCH3", "1.154", "(0.843–1.579)", "0.371"], ["PCMTD2", "1.564", "(0.941–2.600)", "0.085"], ["PITX1", "1.041", "(0.865–1.253)", "0.669"], ["PPAPDC1B", "0.898", "(0.597–1.351)", "0.607"], ["PTBP2", "1.043", "(0.645–1.688)", "0.863"], ["PTPN18", "1.392", "(0.959–2.021)", "0.082"], ["QPRT", "1.182", "(1.003–1.393)", "0.046"], ["RAD1", "0.725", "(0.421–1.249)", "0.246"], ["RRBP1", "1.037", "(0.591–1.821)", "0.900"], ["RSU1", "0.961", "(0.593–1.555)", "0.870"], ["SARDH", "0.732", "(0.593–0.904)", "0.004"], ["SFRS18", "1.506", "(0.844–2.690)", "0.166"], ["SHOX2", "1.143", "(0.961–1.361)", "0.132"], ["SLC16A1", "0.968", "(0.776–1.206)", "0.769"], ["SSRP1", "0.854", "(0.435–1.675)", "0.646"], ["STRAP", "1.562", "(0.839–2.907)", "0.160"], ["SUZ12", "1.792", "(1.030–1.361)", "0.039"], ["TBXA2R", "0.961", "(0.679–1.361)", "0.823"], ["TCF7L1", "1.018", "(0.818–1.266)", "0.876"], ["TNFAIP6", "0.925", "(0.702–1.219)", "0.580"], ["TOX3", "0.999", "(0.895–1.114)", "0.978"], ["TRAFD1", "0.892", "(0.557–1.429)", "0.635"], ["VCPIP1", "0.996", "(0.402–2.469)", "0.994"], ["YIF1A", "2.197", "(1.148–4.207)", "0.018"], ["ZBTB7B", "1.143", "(0.732–1.784)", "0.558"], ["ZCCHC7", "0.695", "(0.415–1.164)", "0.167"]], "row_count": 71, "column_count": 4, "numeric_cells": 222, "header_rows": 1, "locator": "section[9]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:31552180:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7ba6f1d3a861da44ef40784cad9d327b6f469bcdfd3c6107308e4f1b599e774a", "bytes": 993, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[2]#T3", "version": null, "note": "Gene IDs of 12-gene panel.", "structure": {"pmcid": "PMC6743371", "section_index": 9, "section_title": "Gene List Discovery Using TCGA Database", "row_count": 13, "column_count": 3}, "table": {"label": "Table 3", "caption": "Gene IDs of 12-gene panel.", "rows": [["Official gene symbol", "Full name", "UniGene"], ["C6orf62", "Chromosome 6 open reading frame 62", "Hs.744857"], ["YIF1A", "Yip1 interacting factor homolog A", "Hs.446445"], ["ADRBK2", "Adrenergic, beta, receptor kinase 2", "Hs.657494"], ["CYFIP2", "Cytoplasmic FMR1 interacting protein 2", "Hs.519702"], ["ATIC", "5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase", "Hs.90280"], ["QPRT", "Quinolinate phosphoribosyltransferase", "Hs.513484"], ["EHBP1", "EH domain binding protein 1", "Hs.271667"], ["MARCH7", "Membrane-associated ring finger (C3HC4) 7, E3 ubiquitin protein ligase", "Hs.529272"], ["CPA4", "Carboxypeptidase A4", "Hs.93764"], ["SUZ12", "SUZ12 polycomb repressive complex 2 subunit", "Hs.462732"], ["EGFR", "Epidermal growth factor receptor", "Hs.488293"], ["SARDH", "Sarcosine dehydrogenase", "Hs.198003"]], "row_count": 13, "column_count": 3, "numeric_cells": 21, "header_rows": 1, "locator": "section[9]/table-wrap[2]#T3"}}, {"id": "asset:table:pmid:31552180:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:69426ebdfd960f3a2deb20dd7b8159e2e3631c34aed123e6abcf0aca59d27fa4", "bytes": 1189, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#T4", "version": null, "note": "Cox hazard ratio analysis of 12-gene signature and OS in FUSCC cohort.", "structure": {"pmcid": "PMC6743371", "section_index": 10, "section_title": "Validation of the Integrated Gene Signature in the FUSCC Cohort", "row_count": 14, "column_count": 7}, "table": {"label": "Table 4", "caption": "Cox hazard ratio analysis of 12-gene signature and OS in FUSCC cohort.", "rows": [["Gene name", "Univariate", "Multivariate"], ["", "HR", "95%CI", "P", "HR", "95%CI", "P"], ["ADRBK2", "0.704", "0.515–0.961", "0.027", "0.727", "0.499–1.061", "0.100"], ["ATIC", "1.680", "1.224–2.305", "0.001", "1.269", "0.775–2.079", "0.346"], ["CYFIP2", "1.658", "1.198–2.294", "0.002", "1.083", "0.635–1.849", "0.770"], ["C6orf62", "0.621", "0.441–0.874", "0.006", "0.807", "0.543–1.199", "0.290"], ["CPA4", "0.664", "0.468–0.942", "0.022", "0.736", "0.510–1.060", "0.101"], ["EHBP1", "1.788", "1.276–2.505", "0.001", "1.644", "1.160–2.330", "0.006"], ["EGFR", "1.720", "1.241–2.383", "0.001", "1.202", "0.746–1.938", "0.452"], ["MARCH7", "0.636", "0.474–0.853", "0.003", "0.830", "0.579–1.194", "0.318"], ["SARDH", "0.510", "0.339–0.766", "0.001", "0.390", "0.244–0.623", "0.000"], ["SUZ12", "1.508", "1.046–2.174", "0.028", "1.075", "0.739–1.578", "0.715"], ["QPRT", "2.019", "1.427–2.856", "0.000", "1.501", "1.003–2.247", "0.050"], ["YIF1A", "1.972", "1.400–2.778", "0.000", "1.624", "1.061–2.488", "0.027"]], "row_count": 14, "column_count": 7, "numeric_cells": 76, "header_rows": 2, "locator": "section[10]/table-wrap[1]#T4"}}, {"id": "asset:table:pmid:31552180:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5c632b6459babf630e10f8a44b40665e3a5e0676268c12db7a0147aad4b201ad", "bytes": 379, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#T5", "version": null, "note": "C-indexes of Clinical and 12-gene panel prognostic model.", "structure": {"pmcid": "PMC6743371", "section_index": 12, "section_title": "The 12-gene Signature in MIBC Improved the Predictive Value of the Clinical Model", "row_count": 4, "column_count": 4}, "table": {"label": "Table 5", "caption": "C-indexes of Clinical and 12-gene panel prognostic model.", "rows": [["", "TCGA cohort", "FUSCC cohort", "GEO cohort"], ["Clinical data", "0.667", "0.631", "0.772"], ["12-gene panel", "0.741", "0.727", "0.770"], ["Combined model", "0.768", "0.757", "0.880"]], "row_count": 4, "column_count": 4, "numeric_cells": 10, "header_rows": 1, "locator": "section[12]/table-wrap[1]#T5"}}], "gaps": ["asset:data:geo:GSE13507 not downloaded", "asset:data:geo:GSE13507 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": "For the data obtained by qRT-PCR, univariate and multivariate Cox regression models were used for the selection of genes for the predictive gene signature."}}, {"id": "method-2", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.8, "band": "high", "quote": "ROC curve"}}], "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": ["GSE13507"], "resolved_accessions": ["GSE13507"], "statements": ["All datasets generated for this study are included in the manuscript and/or the Supplementary Files."], "basis": "The paper names GSE13507 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:31552180", "data:geo:GSE13507", "asset:table:pmid:31552180:1", "asset:table:pmid:31552180:2", "asset:table:pmid:31552180:3", "asset:table:pmid:31552180:4", "asset:table:pmid:31552180:5"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE13507"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:16:13Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 27911, "completion_tokens": 1492, "cached_tokens": 9480}}, "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:31552180", "type": "paper", "label": "pmid:31552180"}, {"id": "source:pmid:31552180", "type": "manuscript", "label": "PMID 31552180 full text"}, {"id": "data:geo:GSE13507", "type": "dataset", "label": "GEO GSE13507"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31552180", "type": "paper", "label": "pmid:31552180"}, {"id": "source:pmid:31552180", "type": "manuscript", "label": "PMID 31552180 full text"}, {"id": "data:geo:GSE13507", "type": "dataset", "label": "GEO GSE13507"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31552180", "type": "extraction", "used": ["source:pmid:31552180"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE13507", "type": "accession_resolution", "used": ["data:geo:GSE13507"], "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:31552180", "parent_hash": "sha256:c6dc12bd3525ca04e4acfc69633a5b23b17cc57d92541bed2272b5d118c5a520", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE13507 licence not read", "asset:data:geo:GSE13507 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["alyses). By integrating these genes with the RT-qPCR data in our validation dataset and GEO datas", "ses). By integrating these genes with the RT-qPCR data in our validation dataset and GEO datas"], "order_basis": "paper_text_order:1142", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["For the data obtained by qRT-PCR, univariate and multivariate Cox regression models were used for the selection of genes for the predictive gene signature."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}