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Bioinformatics Advance Access published online on May 14, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth215
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received December 17, 2003
Revised March 18, 2004
Accepted March 23, 2004

Applications note

Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data

Ritu Pandey 1*, Raghavendra K. Guru 1, David W. Mount 1*

1 Bioinformatics Core, Arizona Cancer Center, University of Arizona, Tucson, AZ, 85724, USA

* To whom correspondence should be addressed. E-mail: mount{at}email.arizona.edu.


  Abstract

Summary: We have developed a web based system (Pathway Miner) for visualizing gene expression profiles in the context of biological pathways. Pathway Miner catalogs genes based on their role in metabolic, cellular and regulatory pathways. A Fisher exact test is provided as an option to rank pathways. The genes are mapped on to pathways and gene product association networks are extracted for genes that co-occur in pathways. The networks can be filtered for analysis based on user selected options.

Availability: Pathway miner is a freely available, web accessible tool at http://www.biorag.org/pathway.html


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