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Title

 

 

 

 

GS2PATH: A web-based integrated analysis tool for finding functional relationships using gene ontology and biochemical pathway data

 

Authors

Jin Ok Yang1, Charny Park1, Byungwook Lee1, Sangsoo Kim2, Jong Bhak1, *, Hyun Goo Woo3

 

Affiliation

1Korean BioInformation Center, KRIBB, Daejeon 305-806, Korea; 2Department of Bioinformatics, Soongsil University, Seoul, Korea; 3Laboratory of Experimental Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA

 

Email

jong@kribb.re.kr; * Corresponding author

 

Article Type

Web Server

 

Date

received November 30, 2007; revised December 07, 2007; accepted December 30, 2007; published online December 30, 2007

Abstract

GS2PATH is a Web-based pipeline tool to permit functional enrichment of a given gene set from prior knowledge databases, including gene ontology (GO) database and biological pathway databases. The tool also provides an estimation of gene set enrichment, in GO terms, from the databases of the KEGG and BioCarta pathways, which may allow users to compute and compare functional over-representations. This is especially useful in the perspective of biological pathways such as metabolic, signal transduction, genetic information processing, environmental information processing, cellular process, disease, and drug development. It provides relevant images of biochemical pathways with highlighting of the gene set by customized colors, which can directly assist in the visualization of functional alteration.

 

Availability

The GS2PATH system is freely available at http://array.kobic.re.kr:8080/arrayport/gs2path/.

Keywords

gene set enrichment test; gene ontology; pathways; integrated search

 

Citation

Yang et al., Bioinformation 2(5): 194-196 (2007)

 

Edited by

T. Nandi, H. Tan, T. W. Tan & S. Ranganathan

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.