{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,16]],"date-time":"2026-05-16T14:38:52Z","timestamp":1778942332184,"version":"3.51.4"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2019,6,22]],"date-time":"2019-06-22T00:00:00Z","timestamp":1561161600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Technology Innovation Program of the Ministry of Trade, Industry and Energy","award":["10050154"],"award-info":[{"award-number":["10050154"]}]},{"DOI":"10.13039\/100011512","name":"National Research Foundation","doi-asserted-by":"publisher","award":["NRF-2018M3C9A5064705"],"award-info":[{"award-number":["NRF-2018M3C9A5064705"]}],"id":[{"id":"10.13039\/100011512","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Republic of Korea"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Predictive biomarkers for patient stratification play critical roles in realizing the paradigm of precision medicine. Molecular characteristics such as somatic mutations and expression signatures represent the primary source of putative biomarker genes for patient stratification. However, evaluation of such candidate biomarkers is still cumbersome and requires multistep procedures especially when using massive public omics data. Here, we present an interactive web application that divides patients from large cohorts (e.g. The Cancer Genome Atlas, TCGA) dynamically into two groups according to the mutation, copy number variation or gene expression of query genes. It further supports users to examine the prognostic value of resulting patient groups based on survival analysis and their association with the clinical features as well as the previously annotated molecular subtypes, facilitated with a rich and interactive visualization. Importantly, we also support custom omics data with clinical information.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>CaPSSA (Cancer Patient Stratification and Survival Analysis) runs on a web-browser and is freely available without restrictions at http:\/\/www.kobic.re.kr\/capssa\/. The source code is available on https:\/\/github.com\/yjjang\/capssa.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz516","type":"journal-article","created":{"date-parts":[[2019,6,18]],"date-time":"2019-06-18T11:10:36Z","timestamp":1560856236000},"page":"5341-5343","source":"Crossref","is-referenced-by-count":17,"title":["CaPSSA: visual evaluation of cancer biomarker genes for patient stratification and survival analysis using mutation and expression data"],"prefix":"10.1093","volume":"35","author":[{"given":"Yeongjun","family":"Jang","sequence":"first","affiliation":[{"name":"Ewha Research Center for Systems Biology (ERCSB), Ewha Womans University , Seoul 03760, Korea"},{"name":"Interdisciplinary Program in Bioinformatics, College of Natural Science, Seoul National University , Seoul 08826, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jihae","family":"Seo","sequence":"additional","affiliation":[{"name":"Ewha Research Center for Systems Biology (ERCSB), Ewha Womans University , Seoul 03760, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Insu","family":"Jang","sequence":"additional","affiliation":[{"name":"Korean Bioinformation Center (KOBIC) , KRIBB, Daejeon 34141, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Byungwook","family":"Lee","sequence":"additional","affiliation":[{"name":"Korean Bioinformation Center (KOBIC) , KRIBB, Daejeon 34141, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sun","family":"Kim","sequence":"additional","affiliation":[{"name":"Interdisciplinary Program in Bioinformatics, College of Natural Science, Seoul National University , Seoul 08826, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sanghyuk","family":"Lee","sequence":"additional","affiliation":[{"name":"Ewha Research Center for Systems Biology (ERCSB), Ewha Womans University , Seoul 03760, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,6,22]]},"reference":[{"key":"2023013108411838300_btz516-B1","doi-asserted-by":"crossref","first-page":"e74250.","DOI":"10.1371\/journal.pone.0074250","article-title":"SurvExpress: an online biomarker validation tool and database for cancer gene expression data using survival analysis","volume":"8","author":"Aguirre-Gamboa","year":"2013","journal-title":"PLoS One"},{"key":"2023013108411838300_btz516-B2","doi-asserted-by":"crossref","first-page":"45.","DOI":"10.1186\/s13059-015-0612-6","article-title":"Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations","volume":"16","author":"Babur","year":"2015","journal-title":"Genome Biol"},{"key":"2023013108411838300_btz516-B3","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1101\/gr.125567.111","article-title":"Mutual exclusivity analysis identifies oncogenic network modules","volume":"22","author":"Ciriello","year":"2012","journal-title":"Genome Res"},{"key":"2023013108411838300_btz516-B4","doi-asserted-by":"crossref","DOI":"10.1201\/b18041","volume-title":"Modelling Survival Data in Medical Research","author":"Collett","year":"2015","edition":"3"},{"key":"2023013108411838300_btz516-B5","doi-asserted-by":"crossref","DOI":"10.1126\/scisignal.2004088","article-title":"Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal","volume":"6","author":"Gao","year":"2013","journal-title":"Sci. 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