Discover significant associations of orthologous simple sequence repeat patterns with gene ontology terms

Several simple sequence repeats (SSRs) have been demonstrated to regulate gene functions, and SSR mutations in a disease gene may cause different genetic disorders. In order to identify putative functional SSR patterns, a Web system for discovering significant associations between SSR motifs and gene ontology (GO) terms was developed in this study. The system is named as GOSH: Gene Ontology SSR Hierarchy. GOSH employed the GO hierarchy term structure to facilitate users to select a functional or biological gene subset. Significant SSR patterns can be retrieved and identified by a comprehensive over representation analysis within a target gene subset and comparing the results with orthologous genes. Pattern relationship between different biological subsets or supersets can be observed by GO hierarchy structure directly. GOSH also supports gene ontology search through identified significant SSR patterns, and all GO terms possessing specific significant SSR patterns are listed for referencing. The proposed GOSH system is the first comprehensive and efficient online mining tool for discovering significant orthologous SSR patterns with gene ontology terms. The system is available at: http://gosh.cs.ntou.edu.tw.