Separation of biological conditions as determined by PCA in the native compendium (all genes) vs. different gene signature subsets. Clustering and separation of samples along PC1 as well as percentage variance explained by PC1 (in parentheses) were used as indicators of signature effectiveness. (A) PCA of native compendium (all genes). (B) PCA of Fisher's summary statistic-derived digital signature profiles. (C) PCA of module map-derived digital signature profiles. (D) PCA of z-test-derived analog signature profiles.