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

Chien Ming Chen; Chia Sheng Chuang; Zhen Li Huang; Tun Wen Pai

doi:10.1109/BIBMW.2009.5332096

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

Chien Ming Chen
, Chia Sheng Chuang
, Zhen Li Huang
, Tun Wen Pai

Department of Computer Science and Information Engineering

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

1 Scopus citations

Abstract

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.

Original language	English
Title of host publication	Proceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009
Pages	209-213
Number of pages	5
DOIs	https://doi.org/10.1109/BIBMW.2009.5332096
State	Published - 2009
Event	2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009 - Washington, DC, United States Duration: 1 Nov 2009 → 4 Nov 2009

Publication series

Name	Proceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009

Conference

Conference	2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009
Country/Territory	United States
City	Washington, DC
Period	1/11/09 → 4/11/09

Keywords

Comparative genomics
Gene ontology
Homologous gene
Simple sequence repeat

Access to Document

10.1109/BIBMW.2009.5332096

Cite this

Chen, C. M., Chuang, C. S., Huang, Z. L., & Pai, T. W. (2009). Discover significant associations of orthologous simple sequence repeat patterns with gene ontology terms. In Proceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009 (pp. 209-213). Article 5332096 (Proceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009). https://doi.org/10.1109/BIBMW.2009.5332096

Chen, Chien Ming ; Chuang, Chia Sheng ; Huang, Zhen Li et al. / Discover significant associations of orthologous simple sequence repeat patterns with gene ontology terms. Proceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009. 2009. pp. 209-213 (Proceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009).

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title = "Discover significant associations of orthologous simple sequence repeat patterns with gene ontology terms",

abstract = "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.",

keywords = "Comparative genomics, Gene ontology, Homologous gene, Simple sequence repeat",

author = "Chen, \{Chien Ming\} and Chuang, \{Chia Sheng\} and Huang, \{Zhen Li\} and Pai, \{Tun Wen\}",

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Chen, CM, Chuang, CS, Huang, ZL & Pai, TW 2009, Discover significant associations of orthologous simple sequence repeat patterns with gene ontology terms. in Proceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009., 5332096, Proceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009, pp. 209-213, 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009, Washington, DC, United States, 1/11/09. https://doi.org/10.1109/BIBMW.2009.5332096

Discover significant associations of orthologous simple sequence repeat patterns with gene ontology terms. / Chen, Chien Ming; Chuang, Chia Sheng; Huang, Zhen Li et al.
Proceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009. 2009. p. 209-213 5332096 (Proceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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N2 - 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.

AB - 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.

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Chen CM, Chuang CS, Huang ZL, Pai TW. Discover significant associations of orthologous simple sequence repeat patterns with gene ontology terms. In Proceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009. 2009. p. 209-213. 5332096. (Proceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009). doi: 10.1109/BIBMW.2009.5332096

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

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