Mapping biological pathways at a molecular level is a major goal of the post-genome era, providing the functional information required for treating complex disorders. The protein-protein interactions that define a pathway may be measured directly, for example through large-scale yeast-two-hybrid experiments; alternately, correlations in mRNA levels may be used to infer functional relationships. We compare the pathways identified through protein-protein interactions and through mRNA co-regulation. We also describe advances in assessing the statistical significance of gene groupings identified through hierarchical clustering. Finally, we discuss the design of genome-wide, SNP-based association studies.
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