CaPSSA: visual evaluation of cancer biomarker genes for patient stratification and survival analysis using mutation and expression data

Cited 11 time in scopus
Metadata Downloads

Full metadata record

DC FieldValueLanguage
dc.contributor.authorY Jang-
dc.contributor.authorJ Seo-
dc.contributor.authorInsu Jang-
dc.contributor.authorByungwook Lee-
dc.contributor.authorS Kim-
dc.contributor.authorS Lee-
dc.date.accessioned2020-02-07T16:31:02Z-
dc.date.available2020-02-07T16:31:02Z-
dc.date.issued2019-
dc.identifier.issn1367-4803-
dc.identifier.uri10.1093/bioinformatics/btz516ko
dc.identifier.urihttps://oak.kribb.re.kr/handle/201005/19278-
dc.description.abstractSUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: 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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.-
dc.publisherOxford Univ Press-
dc.titleCaPSSA: visual evaluation of cancer biomarker genes for patient stratification and survival analysis using mutation and expression data-
dc.title.alternativeCaPSSA: visual evaluation of cancer biomarker genes for patient stratification and survival analysis using mutation and expression data-
dc.typeArticle-
dc.citation.titleBioinformatics-
dc.citation.number24-
dc.citation.endPage5343-
dc.citation.startPage5341-
dc.citation.volume35-
dc.contributor.affiliatedAuthorInsu Jang-
dc.contributor.affiliatedAuthorByungwook Lee-
dc.contributor.alternativeName장영준-
dc.contributor.alternativeName서지혜-
dc.contributor.alternativeName장인수-
dc.contributor.alternativeName이병욱-
dc.contributor.alternativeName김선-
dc.contributor.alternativeName이상혁-
dc.identifier.bibliographicCitationBioinformatics, vol. 35, no. 24, pp. 5341-5343-
dc.identifier.doi10.1093/bioinformatics/btz516-
dc.description.journalClassY-
Appears in Collections:
1. Journal Articles > Journal Articles
Files in This Item:
  • There are no files associated with this item.


Items in OpenAccess@KRIBB are protected by copyright, with all rights reserved, unless otherwise indicated.