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Database Commons - TSGene

TSGene

Citations: 89

z-index 3.20

Short name TSGene
Full name tumor suppressor gene database
Description TSGene is a comprehensive literature-based database called TSGene (tumor suppressor gene database)
URL http://bioinfo.mc.vanderbilt.edu/TSGene/
Year founded 2012
Last update & version NA    v2.0
Availability Free to all users
University/Institution hosted Vanderbilt University
Address Department of Biomedical Informatics,Vanderbilt University School of Medicine,Nashville,TN 37232,USA
City Nashville
Province/State TN
Country/Region United States
Contact name Zhongming Zhao
Contact email zhongming.zhao@vanderbilt.edu
Data type(s)
Major organism(s)
Keyword(s)
  • cancer mutation
  • tumor suppressor gene
Publication(s)
  • TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes. [PMID: 26590405]

    Min Zhao, Pora Kim, Ramkrishna Mitra, Junfei Zhao, Zhongming Zhao
    Nucleic acids research 2016:44(D1)
    Citation (to be updated)

    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. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  • TSGene: a web resource for tumor suppressor genes. [PMID: 23066107]

    Min Zhao, Jingchun Sun, Zhongming Zhao
    Nucleic acids research 2013:41(Database issue)
    89 Citations (Google Scholar as of 2016-01-29)

    Abstract: Tumor suppressor genes (TSGs) are guardian genes that play important roles in controlling cell proliferation processes such as cell-cycle checkpoints and inducing apoptosis. Identification of these genes and understanding their functions are critical for further investigation of tumorigenesis. So far, many studies have identified numerous TSGs and illustrated their functions in various types of tumors or normal samples. Furthermore, accumulating evidence has shown that non-coding RNAs can act as TSGs to prevent the tumorigenesis processes. Therefore, there is a growing demand to integrate TSGs with large-scale experimental evidence (e.g. gene expression and epigenetic signatures) to provide a comprehensive resource for further investigation of TSGs and their molecular mechanisms in cancer. To achieve this goal, we first developed a comprehensive literature-based database called TSGene (tumor suppressor gene database), freely available at http://bioinfo.mc.vanderbilt.edu/TSGene/. In the current release, TSGene contains 716 human (637 protein-coding and 79 non-coding genes), 628 mouse and 567 rat TSGs curated from UniProtKB, the Tumor Associated Gene database and 5795 PubMed abstracts. Additionally, the TSGene provides detailed annotations for each TSG, such as cancer mutations, gene expressions, methylation sites, TF regulations and protein-protein interactions.

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Tags

Disease DNA Expression Interaction and Network
Homo sapiens Mus musculus Rattus norvegicus
cancer mutation tumor suppressor gene

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Mengwei Li [2016-02-15]
    • Lin Liu [2016-01-29]
    • Lin Liu [2016-01-03]
    • Guangyu Wang [2015-12-06]
    • Guangyu Wang [2015-06-26]
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