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

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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 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