Journal article
TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes
Nucleic Acids Research, Vol.44(D1), pp.D1023-D1031
2016
PMCID: PMC4702895
PMID: 26590405
Abstract
Tumor suppressor genes (TSGs) are a major type of gatekeeper genes in the cell growth. A knowledgebase with the systematic collection and curation of TSGs in multiple cancer types is critically important for further studying their biological functions as well as for developing therapeutic strategies. Since its development in 2012, the Tumor Suppressor Gene database (TSGene), has become a popular resource in the cancer research community. Here, we reported the TSGene version 2.0, which has substantial updates of contents (e.g. up-to-date literature and pan-cancer genomic data collection and curation), data types (noncoding RNAs and protein-coding genes) and content accessibility. Specifically, the current TSGene 2.0 contains 1217 human TSGs (1018 protein-coding and 199 non-coding genes) curated from over 9000 articles. Additionally, TSGene 2.0 provides thousands of expression and mutation patterns derived from pan-cancer data of The Cancer Genome Atlas. A new web interface is available at http://bioinfo.mc.vanderbilt.edu/TSGene/. Systematic analyses of 199 non-coding TSGs provide numerous cancer-specific non-coding mutational events for further screening and clinical use. Intriguingly, we identified 49 protein-coding TSGs that were consistently down-regulated in 11 cancer types. In summary, TSGene 2.0, which is the only available database for TSGs, provides the most updated TSGs and their features in pan-cancer.
Details
- Title
- TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes
- Authors
- Min Zhao (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and EngineeringPora Kim (Author) - Vanderbilt University School of Medicine, United StatesRamkrishna Mitra (Author) - Vanderbilt University School of Medicine, United StatesJunfei Zhao (Author) - Vanderbilt University School of Medicine, United StatesZhongming Zhao (Author) - Vanderbilt University School of Medicine, United States
- Publication details
- Nucleic Acids Research, Vol.44(D1), pp.D1023-D1031
- Publisher
- Oxford University Press
- Date published
- 2016
- DOI
- 10.1093/nar/gkv1268
- ISSN
- 0305-1048
- PMID
- 26590405; PMC4702895
- Copyright note
- Copyright © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
- Organisation Unit
- School of Science and Engineering - Legacy; University of the Sunshine Coast, Queensland; School of Science, Technology and Engineering; Centre for Bioinnovation
- Language
- English
- Record Identifier
- 99449364702621
- Output Type
- Journal article
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