Identifying significant associations of orthologous simple sequence repeats with gene ontologies.
Simple Sequence Repeats (SSRs), also known as microsatellites, regulate gene functions. SSR mutations in a disease gene may cause various genetic disorders. To identify putative functional SSRs, a web-based system, Gene Ontology SSR Hierarchy (GOSH), was developed to facilitate discovery of significant associations between SSRs and Gene Ontology (GO) terms. Using the GO hierarchy term structure, GOSH assists users with selecting functional or biological gene subsets. Significant SSR patterns are retrieved and identified via comprehensive overrepresentation analysis within a target gene subset and by comparing results with orthologous genes. Pattern relationships between different biological subsets or supersets can be observed by using the GO hierarchy structure directly. GOSH also supports GO searching through identified significant SSR patterns and all GO terms possessing such patterns are listed for consultation. GOSH is the first comprehensive and efficient online mining tool for discovering significant orthologous SSR patterns in GO terms and is available at http://gosh.cs.ntou.edu.tw/.
Chien-Ming
CM
Chen
Tun-Wen
TW
Pai
Chia-Sheng
CS
Chuang
Jhen-Li
JL
Huang
Wen-Shyong
WS
Tzou
Chin-Hua
CH
Hu
D057225:Data Mining / Q000379:methods*; D003628:Database Management Systems; D030541:Databases, Genetic; D063990:Gene Ontology; D018895:Microsatellite Repeats / Q000235:genetics*; D009323:Natural Language Processing; D017422:Sequence Analysis, DNA / Q000379:methods*; D017385:Sequence Homology