Pathway Processor 2.0 is an evolution and an improvement over the original Pathway Processor (Grosu P et al., 2002) to allow researchers to analyze microarray and RNAseq data sets with a pathway based logic.

Pathway Processor 2.0 offers two distinct ways of operation. The first relies on the downstream analysis of differentially expressed genes from microarray or RNAseq experiments, using either classic approaches like the Fisher's Exact Test or topology-aware methods like impact analysis (Draghici et al., 2007).

The second way of operation is entirely pathway-driven and uses a recently developed algorithm, Gene Set Variation Analysis (GSVA) to transform microarray or RNAseq gene-based data into pathway-based data which can then be used to compare phenotypes of interest to determine differentially regulated pathways (DRPs).

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