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

Ritu Pandey; Raghavendra K Guru; David W Mount

doi:10.1093/bioinformatics/bth215

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

Bioinformatics. 2004 Sep 1;20(13):2156-8. doi: 10.1093/bioinformatics/bth215. Epub 2004 May 14.

Authors

Ritu Pandey¹, Raghavendra K Guru, David W Mount

Affiliation

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

PMID: 15145817
DOI: 10.1093/bioinformatics/bth215

Abstract

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

Publication types

Research Support, U.S. Gov't, P.H.S.

MeSH terms

Algorithms*
Computer Graphics
Computer Simulation
Gene Expression Regulation / physiology*
Internet
Models, Biological*
Oligonucleotide Array Sequence Analysis / methods*
Online Systems
Protein Interaction Mapping / methods*
Signal Transduction / physiology*
User-Computer Interface*

Grants and funding

P30 CA023074/CA/NCI NIH HHS/United States