We recommend the following open-source tools:
PathVisio is a pathway analysis tool that allows you to draw, edit and analyze biological pathways.
GO-Elite identifies a minimal non-redundant set of biological ontology terms or pathways to describe a particular set of genes or metabolites.
Cytoscape is a software platform for visualizing complex networks and integrating these with any type of attribute data.
WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways.
AltAnalyze is an application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms, AltAnalyze will assess alternative exon expression along protein isoforms, domain composition and microRNA targeting.