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Gene functional similarity search tool (GFSST).
Peisen Zhang1, Jinghui Zhang, Huitao Sheng
1Laboratory of Population Genetics, National Cancer Institute, NIH, Bethesda, USA. zhangpeis@mail.nih.gov
BMC Bioinformatics
|March 16, 2006
Summary
A new Gene Functional Similarity Search Tool (GFSST) helps researchers find genes with similar functions using Gene Ontology (GO) data. This tool aids in selecting candidate genes for disease research and drug discovery from proteome databases.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- High-throughput functional genomics technologies have led to the discovery of numerous genes and their functions.
- Vast amounts of gene and protein data are stored in databases, necessitating efficient retrieval methods.
- Gene Ontology (GO) provides structured vocabularies for gene functions, enabling functional similarity searches.
Purpose of the Study:
- To develop a novel search engine for retrieving genes based on their functions from proteome databases.
- To facilitate the selection of candidate genes for various research applications, including gene-disease studies and biomarker discovery.
Main Methods:
- Utilized a statistical model to quantify functional similarity between genes.
- Employed the Gene Ontology directed acyclic graph for similarity measurement.
- Developed the Gene Functional Similarity Search Tool (GFSST).
Main Results:
- GFSST enables users to search for genes based on desired functions.
- The tool identifies genes with related functions from annotated proteome databases.
- GFSST supports searching by one or multiple GO terms.
Conclusions:
- GFSST is implemented and available via a web server for human and mouse proteomes.
- The tool offers powerful capabilities for retrieving functionally similar genes and gene products.
- Represents a significant advancement in functional gene retrieval from proteomic data.