TSVdb: a Web-tool for TCGA Splicing Variants Analysis

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2018 May 31

PMID 29843604

Citations 62

Authors

Wenjie Sun

Ting Duan

Panmeng Ye

Kelie Chen

Guanling Zhang

Maode Lai

Honghe Zhang

Affiliations

Soon will be listed here.

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.

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