These two questions in BioStar would be helpful, if you want to visualize what you are interested in on pathways.
http://biostar.stackexchange.com/questions/13361/overlaying-gene-expression-results-on-metabolic-pathways
http://biostar.stackexchange.com/questions/4813/tools-for-visualizing-significantly-altered-pathways-and-related-genes-in-a-pathw
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