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TSVdb: a web-tool for TCGA splicing variants analysis
- Source :
- BMC Genomics, Vol 19, Iss 1, Pp 1-7 (2018)
- Publication Year :
- 2018
- Publisher :
- BMC, 2018.
-
Abstract
- Abstract Background Collaborative projects such as The Cancer Genome Atlas (TCGA) have generated various -omics and clinical data on cancer. Many computational tools have been developed to facilitate the study of the molecular characterization of tumors using data from the TCGA. Alternative splicing of a gene produces splicing variants, and accumulating evidence has revealed its essential role in cancer-related processes, implying the urgent need to discover tumor-specific isoforms and uncover their potential functions in tumorigenesis. Result We developed TSVdb, a web-based tool, to explore alternative splicing based on TCGA samples with 30 clinical variables from 33 tumors. TSVdb has an integrated and well-proportioned interface for visualization of the clinical data, gene expression, usage of exons/junctions and splicing patterns. Researchers can interpret the isoform expression variations between or across clinical subgroups and estimate the relationships between isoforms and patient prognosis. TSVdb is available at http://www.tsvdb.com, and the source code is available at https://github.com/wenjie1991/TSVdb. Conclusion TSVdb will inspire oncologists and accelerate isoform-level advances in cancer research.
Details
- Language :
- English
- ISSN :
- 14712164
- Volume :
- 19
- Issue :
- 1
- Database :
- Directory of Open Access Journals
- Journal :
- BMC Genomics
- Publication Type :
- Academic Journal
- Accession number :
- edsdoj.5d5ccb0d97f641218181ed5975e8c4a9
- Document Type :
- article
- Full Text :
- https://doi.org/10.1186/s12864-018-4775-x