TSVdb: a web-tool for TCGA splicing variants analysis

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...

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Bibliographic Details
Main Authors: Wenjie Sun, Ting Duan, Panmeng Ye, Kelie Chen, Guanling Zhang, Maode Lai, Honghe Zhang
Format: Article
Language:English
Published: BMC 2018-05-01
Series:BMC Genomics
Subjects:
Online Access:http://link.springer.com/article/10.1186/s12864-018-4775-x
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Summary: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.
ISSN:1471-2164