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Nucleic Acids Res. 2016 Jan 4;44(D1):D1023-31. doi: 10.1093/nar/gkv1268. Epub 2015 Nov 20.

TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes.

Author information

1
School of Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia.
2
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
3
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37212, USA School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA zhongming.zhao@vanderbilt.edu.

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.

PMID:
26590405
PMCID:
PMC4702895
DOI:
10.1093/nar/gkv1268
[Indexed for MEDLINE]
Free PMC Article

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