A Semiautomatic Method to Achieve Independent and Intact Gene Ontology Slim (InitGO) and its Cytoscape Plugin Implementation

Author

Liu, Qijun ; Wang, Zhenghua ; Sun, Hanchang ; Guo, Hao ; Liu, Wanlin ; Zhu, Yunping

Author_Institution

Nat. Lab. for Parallel & Distrib. Process., Nat. Univ. of Deference & Technol., Changsha, China

fYear

2009

fDate

17-19 Oct. 2009

Firstpage

1

Lastpage

4

Abstract

To conduct a systemic analysis of biological networks function distribution and function modules, we present a semiautomatic method to achieve independent and intact GO slim (InitGO) based on graph operations and GO hierarchy structure. Our method is packed into a user-friendly Cytoscape plugin named InitGO. The application of InitGO to yeast transcriptional factors regulatory network shows that the network has function modularity, offering evidence that our method is effective for defining function modules. InitGO plugin and source codes are available on request from the authors.

Keywords

biology computing; cellular biophysics; graph theory; ontologies (artificial intelligence); biological networks function distribution; biological networks function modules; cellular functions; cytoscape plugin; graph operations; independent gene ontology slim; intact gene ontology slim; semiautomatic method; yeast transcriptional factors regulatory network; Bioinformatics; Biological information theory; Data visualization; Distributed processing; Fungi; Independent component analysis; Laboratories; Ontologies; Systems biology; Transfer functions;

fLanguage

English

Publisher

ieee

Conference_Titel

Biomedical Engineering and Informatics, 2009. BMEI '09. 2nd International Conference on

Conference_Location

Tianjin

Print_ISBN

978-1-4244-4132-7

Electronic_ISBN

978-1-4244-4134-1

Type

conf

DOI

10.1109/BMEI.2009.5301665

Filename

5301665