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


BACKGROUND
Pathway Miner is a freely available web accessible tool at http://www.biorag.org/pathway.html
Pandey
Ritu
R
Bioinformatics Core, Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA.
Guru
Raghavendra K
RK
Mount
David W
DW
D000465:Algorithms; D003196:Computer Graphics; D003198:Computer Simulation; D005786:Gene Expression Regulation / Q000502:physiology*; D020407:Internet; D008954:Models, Biological; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009862:Online Systems; D025941:Protein Interaction Mapping / Q000379:methods*; D015398:Signal Transduction / Q000502:physiology*; D014584:User-Computer Interface