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- Title
TSVdb: a web-tool for TCGA splicing variants analysis.
- Authors
Sun, Wenjie; Duan, Ting; Ye, Panmeng; Chen, Kelie; Zhang, Guanling; Lai, Maode; Zhang, Honghe
- 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 <ext-link>http://www.tsvdb.com</ext-link>, and the source code is available at <ext-link>https://github.com/wenjie1991/TSVdb</ext-link>. Conclusion: TSVdb will inspire oncologists and accelerate isoform-level advances in cancer research.
- Subjects
GENOMES; CANCER; NEOPLASTIC cell transformation; BIOINFORMATICS; MEDICAL protocols
- Publication
BMC Genomics, 2018, Vol 19, Issue 1, p1
- ISSN
1471-2164
- Publication type
Article
- DOI
10.1186/s12864-018-4775-x