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Bioinformatics Advance Access originally published online on May 14, 2004
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Bioinformatics 20(13) © Oxford University Press 2004; all rights reserved.

Applications Note

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

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

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

Received on December 17, 2003; revised on March 18, 2004; accepted on March 23, 2004
Advance Access Publication May 14, 2004

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 onto 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

Contact: mount{at}email.arizona.edu

* To whom correspondence should be addressed.


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