Gene functional similarity search tool (GFSST)

Peisen Zhang, Jinghui Zhang, Huitao Sheng, James J. Russo, Brian Osborne, Kenneth Buetow

Research output: Contribution to journalArticle

38 Citations (Scopus)

Abstract

Background: With the completion of the genome sequences of human, mouse, and other species and the advent of high throughput functional genomic research technologies such as biomicroarray chips, more and more genes and their products have been discovered and their functions have begun to be understood. Increasing amounts of data about genes, gene products and their functions have been stored in databases. To facilitate selection of candidate genes for gene-disease research, genetic association studies, biomarker and drug target selection, and animal models of human diseases, it is essential to have search engines that can retrieve genes by their functions from proteome databases. In recent years, the development of Gene Ontology (GO) has established structured, controlled vocabularies describing gene functions, which makes it possible to develop novel tools to search genes by functional similarity. Results: By using a statistical model to measure the functional similarity of genes based on the Gene Ontology directed acyclic graph, we developed a novel Gene Functional Similarity Search Tool (GFSST) to identify genes with related functions from annotated proteome databases. This search engine lets users design their search targets by gene functions. Conclusion: An implementation of GFSST which works on the UniProt (Universal Protein Resource) for the human and mouse proteomes is available at GFSST Web Server. GFSST provides functions not only for similar gene retrieval but also for gene search by one or more GO terms. This represents a powerful new approach for selecting similar genes and gene products from proteome databases according to their functions.

Original languageEnglish (US)
Article number135
JournalBMC Bioinformatics
Volume7
DOIs
StatePublished - Mar 14 2006
Externally publishedYes

Fingerprint

Similarity Search
Genes
Gene
Proteome
Gene Ontology
Databases
Proteins
Search Engine
Ontology
Mouse
Search engines
Controlled Vocabulary
Genetic Association
Functional Genomics
Animal Disease Models
Animal Model
Target
Selection Model

ASJC Scopus subject areas

  • Medicine(all)
  • Structural Biology
  • Applied Mathematics

Cite this

Zhang, P., Zhang, J., Sheng, H., Russo, J. J., Osborne, B., & Buetow, K. (2006). Gene functional similarity search tool (GFSST). BMC Bioinformatics, 7, [135]. https://doi.org/10.1186/1471-2105-7-135

Gene functional similarity search tool (GFSST). / Zhang, Peisen; Zhang, Jinghui; Sheng, Huitao; Russo, James J.; Osborne, Brian; Buetow, Kenneth.

In: BMC Bioinformatics, Vol. 7, 135, 14.03.2006.

Research output: Contribution to journalArticle

Zhang, P, Zhang, J, Sheng, H, Russo, JJ, Osborne, B & Buetow, K 2006, 'Gene functional similarity search tool (GFSST)', BMC Bioinformatics, vol. 7, 135. https://doi.org/10.1186/1471-2105-7-135
Zhang, Peisen ; Zhang, Jinghui ; Sheng, Huitao ; Russo, James J. ; Osborne, Brian ; Buetow, Kenneth. / Gene functional similarity search tool (GFSST). In: BMC Bioinformatics. 2006 ; Vol. 7.
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