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PathNet : A tool for finding pathway enrichment and pathway cross-talk using topological information and gene expression data

The Pathway analysis using Network information (PathNet) algorithm, described in Dutta et al., is described here. PathNet uses topological information present in pathways and differential expression levels of genes, obtained from microarray experiments, to identify pathways that are 1) significantly enriched and 2) associated in the context of gene expression data. In enrichment analysis, PathNet considers both the differential expression of genes and their pathway neighbors to strengthen the evidence that a pathway is implicated in the biological conditions characterizing the experiment. In addition, PathNet uses the connectivity of the differentially expressed genes among all pathways to score pathway contextual associations and statistically identify biological relations among pathways.