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

Cited 6 time in scopus
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Title
CaPSSA: visual evaluation of cancer biomarker genes for patient stratification and survival analysis using mutation and expression data
Author(s)
Y Jang; J Seo; Insu JangByungwook Lee; S Kim; S Lee
Bibliographic Citation
Bioinformatics, vol. 35, no. 24, pp. 5341-5343
Publication Year
2019
Abstract
SUMMARY: 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.
ISSN
1367-4803
Publisher
Oxford Univ Press
DOI
http://dx.doi.org/10.1093/bioinformatics/btz516
Type
Article
Appears in Collections:
Korea Bioinformation Center > 1. Journal Articles
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