Journal
BMC GENOMICS
Volume 19, Issue -, Pages -Publisher
BIOMED CENTRAL LTD
DOI: 10.1186/s12864-018-4775-x
Keywords
Splicing variant; Alternative splicing; TCGA; Cancer; Visualization tools
Funding
- National Natural Science Foundation of China [81672730, 81572716]
- 111 Project [B13026]
- Fundamental Research Funds for the Central Universities [172210271]
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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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