Global expression profiling is a promising technique to help uncover perturbations associated with heart disease. With the large amount of expression data generated, we demonstrate how a list of differentially expressed proteins or genes can be translated into a list of perturbed pathways and functions using conventional overrepresentation analysis such as gene set enrichment analysis, DAVID, and BiNGO. As outputs from ORA can be daunting in themselves, we further demonstrate how to visualize enrichment results as Enrichment Maps for easy interpretation and analysis.