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CaPSSA: visual evaluation of cancer biomarker genes for patient stratification and survival analysis using mutation and expression data
- Title
- CaPSSA: visual evaluation of cancer biomarker genes for patient stratification and survival analysis using mutation and expression data
- Authors
- Jang, Yeongjun; Seo, Jihae; Jang, Insu; Lee, Byungwook; Kim, Sun; Lee, Sanghyuk
- Ewha Authors
- 이상혁; 서지혜
- SCOPUS Author ID
- 이상혁; 서지혜
- Issue Date
- 2019
- Journal Title
- BIOINFORMATICS
- ISSN
- 1367-4803
1460-2059
- Citation
- BIOINFORMATICS vol. 35, no. 24, pp. 5341 - 5343
- Publisher
- OXFORD UNIV PRESS
- Indexed
- SCIE; SCOPUS
- Document Type
- Article
- Abstract
- 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.
- DOI
- 10.1093/bioinformatics/btz516
- Appears in Collections:
- 자연과학대학 > 생명과학전공 > Journal papers
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