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TSGene: a web resource for tumor suppressor genes
Min Zhao1, Jingchun Sun, Zhongming Zhao
1Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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.
Insights
Tumor suppressor genes (TSGs) are crucial for preventing cancer. This study introduces TSGene, a database integrating 716 human TSGs with experimental data to aid cancer research.
Area of Science:
- Genomics
- Cancer Biology
- Bioinformatics
Background:
- Tumor suppressor genes (TSGs) regulate cell proliferation, cell-cycle checkpoints, and apoptosis, acting as critical guardians against cancer.
- Non-coding RNAs are increasingly recognized for their tumor-suppressive roles, highlighting the need for comprehensive gene resources.
- Investigating tumorigenesis requires integrated data on TSGs, including gene expression and epigenetic signatures.
Purpose of the Study:
- To develop a comprehensive, literature-based database of tumor suppressor genes (TSGs).
- To integrate TSGs with large-scale experimental evidence for cancer research.
- To provide a valuable resource for investigating TSGs and their molecular mechanisms in cancer.
Main Methods:
- Developed TSGene, a literature-based database of tumor suppressor genes.
- Curated TSG information from UniProtKB, the Tumor Associated Gene database, and PubMed abstracts.
- Integrated data including gene expression, epigenetic signatures, mutations, and regulatory interactions.
Main Results:
- TSGene database currently contains 716 human (637 protein-coding, 79 non-coding), 628 mouse, and 567 rat TSGs.
- Detailed annotations for each TSG include cancer mutations, gene expression, methylation sites, transcription factor regulations, and protein-protein interactions.
- The database is freely available at http://bioinfo.mc.vanderbilt.edu/TSGene/.
Conclusions:
- TSGene provides a comprehensive resource for the study of tumor suppressor genes.
- The integrated data facilitates further investigation into the molecular mechanisms of tumorigenesis.
- This database supports research on cancer biology and the development of targeted therapies.
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