{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T20:48:40Z","timestamp":1791838120178,"version":"4.3.4"},"reference-count":39,"publisher":"Elsevier BV","issue":"6","license":[{"start":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T00:00:00Z","timestamp":1778198400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82273084"],"award-info":[{"award-number":["82273084"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012154","name":"Graduate Research and Innovation Projects of Jiangsu Province","doi-asserted-by":"publisher","award":["KYCX22_3569"],"award-info":[{"award-number":["KYCX22_3569"]}],"id":[{"id":"10.13039\/501100012154","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010909","name":"Excellent Young Scientists Fund","doi-asserted-by":"publisher","award":["82404358"],"award-info":[{"award-number":["82404358"]}],"id":[{"id":"10.13039\/501100010909","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["iScience"],"published-print":{"date-parts":[[2026,6]]},"DOI":"10.1016\/j.isci.2026.116100","type":"journal-article","created":{"date-parts":[[2026,5,22]],"date-time":"2026-05-22T11:46:28Z","timestamp":1779450388000},"page":"116100","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integration of single-cell regulon atlas and bulk RNA-seq for individualized prognostic prediction in stomach adenocarcinoma"],"prefix":"10.1016","volume":"29","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-0821-4079","authenticated-orcid":false,"given":"Aiping","family":"Zhang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhe","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaoyao","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanbing","family":"Ding","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.isci.2026.116100_bib1","first-page":"229","article-title":"Global cancer statistics 2022: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries","volume":"74","author":"Bray","year":"2024","journal-title":"CA Cancer J. Clin."},{"key":"10.1016\/j.isci.2026.116100_bib2","doi-asserted-by":"crossref","first-page":"700","DOI":"10.1158\/1055-9965.EPI-13-1057","article-title":"Gastric cancer: descriptive epidemiology, risk factors, screening, and prevention","volume":"23","author":"Karimi","year":"2014","journal-title":"Cancer Epidemiol. Biomarkers Prev."},{"key":"10.1016\/j.isci.2026.116100_bib3","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.3748\/wjg.v28.i12.1187","article-title":"Epidemiology of stomach cancer","volume":"28","author":"Ilic","year":"2022","journal-title":"World J. Gastroenterol."},{"key":"10.1016\/j.isci.2026.116100_bib4","doi-asserted-by":"crossref","first-page":"800","DOI":"10.1016\/j.ccell.2015.10.003","article-title":"Mist1 Expressing Gastric Stem Cells Maintain the Normal and Neoplastic Gastric Epithelium and Are Supported by a Perivascular Stem Cell Niche","volume":"28","author":"Hayakawa","year":"2015","journal-title":"Cancer Cell"},{"key":"10.1016\/j.isci.2026.116100_bib5","doi-asserted-by":"crossref","first-page":"7007","DOI":"10.7150\/thno.98389","article-title":"BATF2 inhibits the stem cell-like properties and chemoresistance of gastric cancer cells through PTEN\/AKT\/\u03b2-catenin pathway","volume":"14","author":"Cao","year":"2024","journal-title":"Theranostics"},{"key":"10.1016\/j.isci.2026.116100_bib6","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1186\/s13059-019-1713-4","article-title":"Single-cell transcriptomics unveils gene regulatory network plasticity","volume":"20","author":"Iacono","year":"2019","journal-title":"Genome Biol."},{"key":"10.1016\/j.isci.2026.116100_bib7","first-page":"575","article-title":"Gene co-expression analysis for functional classification and gene-disease predictions","volume":"19","author":"van Dam","year":"2018","journal-title":"Brief. Bioinform."},{"key":"10.1016\/j.isci.2026.116100_bib8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s12276-018-0071-8","article-title":"Single-cell RNA sequencing technologies and bioinformatics pipelines","volume":"50","author":"Hwang","year":"2018","journal-title":"Exp. Mol. Med."},{"key":"10.1016\/j.isci.2026.116100_bib9","first-page":"433","article-title":"Spatially resolved expression landscape and gene-regulatory network of human gastric corpus epithelium","volume":"14","author":"Dong","year":"2023","journal-title":"Protein Cell"},{"key":"10.1016\/j.isci.2026.116100_bib10","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1053\/j.gastro.2008.04.019","article-title":"Transcription factor foxq1 controls mucin gene expression and granule content in mouse stomach surface mucous cells","volume":"135","author":"Verzi","year":"2008","journal-title":"Gastroenterology"},{"key":"10.1016\/j.isci.2026.116100_bib11","doi-asserted-by":"crossref","DOI":"10.1084\/jem.20241253","article-title":"Estrogen influences class-switched memory B cell frequency only in humans with two X chromosomes","volume":"222","author":"Peckham","year":"2025","journal-title":"J. Exp. Med."},{"key":"10.1016\/j.isci.2026.116100_bib12","doi-asserted-by":"crossref","first-page":"1336","DOI":"10.1016\/j.ccell.2024.06.006","article-title":"Targeting the mSWI\/SNF complex in POU2F-POU2AF transcription factor-driven malignancies","volume":"42","author":"He","year":"2024","journal-title":"Cancer Cell"},{"key":"10.1016\/j.isci.2026.116100_bib13","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1016\/j.trecan.2023.04.012","article-title":"The conundrum of Helicobacter pylori-associated apoptosis in gastric cancer","volume":"9","author":"Lim","year":"2023","journal-title":"Trends Cancer"},{"key":"10.1016\/j.isci.2026.116100_bib14","doi-asserted-by":"crossref","first-page":"5660","DOI":"10.3748\/wjg.v20.i19.5660","article-title":"Helicobacter pylori eradication for preventing gastric cancer","volume":"20","author":"Lu","year":"2014","journal-title":"World J. Gastroenterol."},{"key":"10.1016\/j.isci.2026.116100_bib15","doi-asserted-by":"crossref","DOI":"10.1016\/j.canlet.2024.216939","article-title":"SOX9 is regulated by AURKA in response to Helicobacter pylori infection via EIF4E-mediated cap-dependent translation","volume":"593","author":"Gomaa","year":"2024","journal-title":"Cancer Lett."},{"key":"10.1016\/j.isci.2026.116100_bib16","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1186\/s12964-023-01127-y","article-title":"Microvesicles from bone marrow-derived mesenchymal stem cells promote Helicobacter pylori-associated gastric cancer progression by transferring thrombospondin-2","volume":"21","author":"Qi","year":"2023","journal-title":"Cell Commun. Signal."},{"key":"10.1016\/j.isci.2026.116100_bib17","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1158\/0008-5472.CAN-17-3155","article-title":"ME1 Regulates NADPH Homeostasis to Promote Gastric Cancer Growth and Metastasis","volume":"78","author":"Lu","year":"2018","journal-title":"Cancer Res."},{"key":"10.1016\/j.isci.2026.116100_bib18","doi-asserted-by":"crossref","first-page":"1909","DOI":"10.7150\/ijbs.57623","article-title":"ESRRA promotes gastric cancer development by regulating the CDC25C\/CDK1\/CyclinB1 pathway via DSN1","volume":"17","author":"Li","year":"2021","journal-title":"Int. J. Biol. Sci."},{"key":"10.1016\/j.isci.2026.116100_bib19","doi-asserted-by":"crossref","first-page":"1850","DOI":"10.1158\/1078-0432.CCR-10-2180","article-title":"Gene expression signature-based prognostic risk score in gastric cancer","volume":"17","author":"Cho","year":"2011","journal-title":"Clin. Cancer Res."},{"key":"10.1016\/j.isci.2026.116100_bib20","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1002\/path.5434","article-title":"Dissecting expression profiles of gastric precancerous lesions and early gastric cancer to explore crucial molecules in intestinal-type gastric cancer tumorigenesis","volume":"251","author":"Zhang","year":"2020","journal-title":"J. Pathol."},{"key":"10.1016\/j.isci.2026.116100_bib21","doi-asserted-by":"crossref","first-page":"8633","DOI":"10.7150\/thno.47938","article-title":"Identification of a Tumor Microenvironment-relevant Gene set-based Prognostic Signature and Related Therapy Targets in Gastric Cancer","volume":"10","author":"Cai","year":"2020","journal-title":"Theranostics"},{"key":"10.1016\/j.isci.2026.116100_bib22","doi-asserted-by":"crossref","first-page":"1806","DOI":"10.1101\/gr.278063.123","article-title":"Multiscale network modeling reveals the gene regulatory landscape driving cancer prognosis in 32 cancer types","volume":"33","author":"Xu","year":"2023","journal-title":"Genome Res."},{"key":"10.1016\/j.isci.2026.116100_bib23","doi-asserted-by":"crossref","first-page":"2019","DOI":"10.1016\/j.ccell.2023.10.004","article-title":"Spatiotemporal genomic profiling of intestinal metaplasia reveals clonal dynamics of gastric cancer progression","volume":"41","author":"Huang","year":"2023","journal-title":"Cancer Cell"},{"key":"10.1016\/j.isci.2026.116100_bib24","doi-asserted-by":"crossref","first-page":"736","DOI":"10.1007\/s00535-011-0396-8","article-title":"The combination of serum trefoil factor 3 and pepsinogen testing is a valid non-endoscopic biomarker for predicting the presence of gastric cancer: a new marker for gastric cancer risk","volume":"46","author":"Kaise","year":"2011","journal-title":"J. Gastroenterol."},{"key":"10.1016\/j.isci.2026.116100_bib25","doi-asserted-by":"crossref","first-page":"5877","DOI":"10.1158\/0008-5472.CAN-18-1011","article-title":"EGR1-Mediated Transcription of lncRNA-HNF1A-AS1 Promotes Cell-Cycle Progression in Gastric Cancer","volume":"78","author":"Liu","year":"2018","journal-title":"Cancer Res."},{"key":"10.1016\/j.isci.2026.116100_bib26","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1186\/s12943-025-02341-7","article-title":"The EGR1-mediated lncRNA TENM3-AS1 potentiates gastric cancer metastasis via reprogramming fatty acid metabolism","volume":"24","author":"Tang","year":"2025","journal-title":"Mol. Cancer"},{"key":"10.1016\/j.isci.2026.116100_bib27","article-title":"ELK3 Controls Gastric Cancer Cell Migration and Invasion by Regulating ECM Remodeling-Related Genes","volume":"23","author":"Lee","year":"2022","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.isci.2026.116100_bib28","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/j.semcancer.2021.04.003","article-title":"Hedgehog signaling mechanism and role in cancer","volume":"85","author":"Jiang","year":"2022","journal-title":"Semin. Cancer Biol."},{"key":"10.1016\/j.isci.2026.116100_bib29","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1016\/j.biopha.2019.01.018","article-title":"GLI1 overexpression promotes gastric cancer cell proliferation and migration and induces drug resistance by combining with the AKT-mTOR pathway","volume":"111","author":"Yao","year":"2019","journal-title":"Biomed. Pharmacother."},{"key":"10.1016\/j.isci.2026.116100_bib30","doi-asserted-by":"crossref","DOI":"10.1172\/JCI179617","article-title":"An inherited predisposition allele promotes gastric cancer via enhancing deubiquitination-mediated activation of epithelial-to-mesenchymal transition signaling","volume":"135","author":"Tao","year":"2025","journal-title":"J. Clin. Investig."},{"key":"10.1016\/j.isci.2026.116100_bib31","doi-asserted-by":"crossref","first-page":"2710","DOI":"10.1002\/jcp.31124","article-title":"CBX8 promotes lung adenocarcinoma growth and metastasis through transcriptional repression of CDKN2C and SCEL","volume":"238","author":"Chen","year":"2023","journal-title":"J. Cell. Physiol."},{"key":"10.1016\/j.isci.2026.116100_bib32","doi-asserted-by":"crossref","first-page":"1934","DOI":"10.1016\/j.celrep.2019.04.052","article-title":"Dissecting the Single-Cell Transcriptome Network Underlying Gastric Premalignant Lesions and Early Gastric Cancer","volume":"27","author":"Zhang","year":"2019","journal-title":"Cell Rep."},{"key":"10.1016\/j.isci.2026.116100_bib33","doi-asserted-by":"crossref","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","article-title":"Integrated analysis of multimodal single-cell data","volume":"184","author":"Hao","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.isci.2026.116100_bib34","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with Harmony","volume":"16","author":"Korsunsky","year":"2019","journal-title":"Nat. Methods"},{"key":"10.1016\/j.isci.2026.116100_bib35","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1053\/j.gastro.2014.09.042","article-title":"In vitro expansion of human gastric epithelial stem cells and their responses to bacterial infection","volume":"148","author":"Bartfeld","year":"2015","journal-title":"Gastroenterology"},{"key":"10.1016\/j.isci.2026.116100_bib36","doi-asserted-by":"crossref","first-page":"2247","DOI":"10.1038\/s41596-020-0336-2","article-title":"A scalable SCENIC workflow for single-cell gene regulatory network analysis","volume":"15","author":"Van de Sande","year":"2020","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.isci.2026.116100_bib37","doi-asserted-by":"crossref","first-page":"1436","DOI":"10.1016\/j.celrep.2018.10.045","article-title":"Revealing the Critical Regulators of Cell Identity in the Mouse Cell Atlas","volume":"25","author":"Suo","year":"2018","journal-title":"Cell Rep."},{"key":"10.1016\/j.isci.2026.116100_bib38","doi-asserted-by":"crossref","first-page":"2798","DOI":"10.1016\/j.csbj.2024.06.035","article-title":"Mime: A flexible machine-learning framework to construct and visualize models for clinical characteristics prediction and feature selection","volume":"23","author":"Liu","year":"2024","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"10.1016\/j.isci.2026.116100_bib39","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1471-2105-14-7","article-title":"GSVA: gene set variation analysis for microarray and RNA-seq data","volume":"14","author":"H\u00e4nzelmann","year":"2013","journal-title":"BMC Bioinf."}],"container-title":["iScience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2589004226014756?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2589004226014756?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T20:36:15Z","timestamp":1791837375000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2589004226014756"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6]]},"references-count":39,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2026,6]]}},"alternative-id":["S2589004226014756"],"URL":"https:\/\/doi.org\/10.1016\/j.isci.2026.116100","relation":{},"ISSN":["2589-0042"],"issn-type":[{"value":"2589-0042","type":"print"}],"subject":[],"published":{"date-parts":[[2026,6]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Integration of single-cell regulon atlas and bulk RNA-seq for individualized prognostic prediction in stomach adenocarcinoma","name":"articletitle","label":"Article Title"},{"value":"iScience","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.isci.2026.116100","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"116100"}}