TABLE S3: SIMES EXTENDED PATHWAY RANKINGS Rank KEGG pathway name pi^path Size Top 100 genes in pathway 1 Oxidative Phosphorylation 0.314 871 ATP12A COX6B2 PPA2 UQCRQ NDUFS4 ATP5J NDUFA10 NDUFA4 NDUFA9 SDHB SDHC ATP6V0A4 2 Terpenoid Backbone Biosynthesis 0.260 158 DHDDS PMVK PDSS2 HMGCS2 3 Regulation Of Autophagy 0.183 215 ATG7 GABARAPL1 4 Glycerolipid Metabolism 0.095 1074 ALDH7A1 ALDH1B1 GPAM DGKB DGKD DGKG DGKH DGKI ALDH2 LIPC 5 Dilated Cardiomyopathy 0.078 3177 ADCY1 ADCY2 ADCY8 CACNG3 ADRB1 SGCG SGCD RYR2 ITGA11 CACNB2 ITGB1 ACTB CACNA2D1 SLC8A1 ITGA1 ITGA2 CACNA2D3 CACNA1S CACNA2D4 LAMA2 ITGA9 CACNA1C CACNA1D 6 Hypertrophic Cardiomyopathy Hcm 0.071 2932 PRKAG2 CACNG3 SGCG SGCD RYR2 ITGA11 CACNB2 ITGB1 ACTB CACNA2D1 SLC8A1 ITGA1 ITGA2 CACNA2D3 CACNA1S CACNA2D4 LAMA2 ITGA9 CACNA1C CACNA1D 7 Ribosome 0.064 270 RPL3L RPL30 8 Glutathione Metabolism 0.055 389 MGST3 MGST1 9 Arrhythmogenic Right Ventricular Cardiomyopathy Arvc 0.053 3899 ACTN1 CACNG3 CTNNA3 CTNNA2 SGCG SGCD RYR2 ITGA11 CACNB2 ITGB1 ACTB CACNA2D1 SLC8A1 ITGA1 ITGA2 CACNA2D3 CACNA1S CACNA2D4 LAMA2 ITGA9 CACNA1C CACNA1D 10 T Cell Receptor Signaling Pathway 0.052 1624 IL10 MAP3K7 KRAS VAV3 MAP2K2 VAV2 VAV1 CBLB PAK7 PAK2 NCK2 PRKCQ PIK3R5 NFATC2 IL4 FYN 11 Cardiac Muscle Contraction 0.047 1952 UQCRQ CACNG3 RYR2 CACNB2 COX6B2 CACNA2D1 SLC8A1 CACNA2D3 CACNA1S CACNA2D4 CACNA1C CACNA1D 12 Biosynthesis Of Unsaturated Fatty Acids 0.047 282 SCD5 13 Lysosome 0.046 1322 LIPA SUMF1 ATP6V0A4 14 Apoptosis 0.044 954 CASP9 IL1R1 IRAK3 BCL2 PIK3R5 15 Pathogenic Escherichia Coli Infection 0.041 538 PRKCA NCK2 ITGB1 ACTB FYN 16 Metabolism Of Xenobiotics By Cytochrome P450 0.039 880 MGST3 MGST1 17 Drug Metabolism Cytochrome P450 0.038 910 MGST3 MGST1 18 Autoimmune Thyroid Disease 0.037 686 IL10 HLA-C IL4 19 Focal Adhesion 0.034 4787 ITGA11 LAMA2 CCND3 BCL2 MAPK10 FYN PDGFD EGFR ACTN1 ITGB1 VAV3 ITGA1 ITGA2 VAV2 VAV1 ITGA9 RAP1A PAK7 PAK2 PRKCA PRKCB IGF1R PIK3R5 ACTB 20 Leishmania Infection 0.034 718 IL10 MAP3K7 PRKCB ITGB1 IL4 21 Ppar Signaling Pathway 0.032 800 SCD5 HMGCS2 22 Rna Polymerase 0.031 193 23 Lysine Degradation 0.030 423 SETMAR ALDH7A1 ALDH1B1 ALDH2 24 Endocytosis 0.030 3436 EGFR HLA-C CBLB ADRB1 IGF1R NEDD4L 25 Glycosaminoglycan Biosynthesis Chondroitin Sulfate 0.029 727 26 Melanoma 0.028 1189 E2F3 PDGFD EGFR IGF1R KRAS PIK3R5 MAP2K2 27 Nucleotide Excision Repair 0.028 330 28 Prostate Cancer 0.026 1419 E2F3 CASP9 PDGFD EGFR IGF1R KRAS BCL2 PIK3R5 MAP2K2 29 Renal Cell Carcinoma 0.026 1004 PAK7 PAK2 KRAS PIK3R5 MAP2K2 RAP1A 30 Glycine Serine And Threonine Metabolism 0.026 268 31 Glycerophospholipid Metabolism 0.025 1283 GPAM DGKB DGKD DGKG DGKH DGKI 32 Steroid Hormone Biosynthesis 0.025 646 33 Steroid Biosynthesis 0.024 174 LIPA 34 Aldosterone Regulated Sodium Reabsorption 0.023 848 KRAS PIK3R5 NEDD4L PRKCA PRKCB 35 Viral Myocarditis 0.023 1174 CASP9 HLA-C SGCG SGCD ACTB LAMA2 FYN 36 Regulation Of Actin Cytoskeleton 0.023 4013 ITGA11 KRAS MAP2K2 PDGFD EGFR ACTN1 ITGB1 VAV3 ITGA1 ITGA2 VAV2 VAV1 ITGA9 PAK7 PAK2 PIK3R5 ACTB 37 Type Ii Diabetes Mellitus 0.023 1292 PIK3R5 MAPK10 CACNA1C CACNA1D 38 Proteasome 0.023 252 39 Linoleic Acid Metabolism 0.022 366 40 Type I Diabetes Mellitus 0.022 814 HLA-C 41 Abc Transporters 0.021 2217 42 Adipocytokine Signaling Pathway 0.021 948 PRKAG2 PRKCQ MAPK10 43 Drug Metabolism Other Enzymes 0.020 810 44 N Glycan Biosynthesis 0.020 699 45 Glycosphingolipid Biosynthesis Globo Series 0.020 249 46 Aminoacyl Trna Biosynthesis 0.019 530 47 Valine Leucine And Isoleucine Degradation 0.019 639 ALDH7A1 HMGCS2 ALDH1B1 ALDH2 48 Oocyte Meiosis 0.018 1857 ADCY1 ADCY2 ADCY8 IGF1R RPS6KA2 49 Glycosaminoglycan Biosynthesis Heparan Sulfate 0.018 671 50 Progesterone Mediated Oocyte Maturation 0.017 1407 ADCY1 ADCY2 ADCY8 IGF1R KRAS PIK3R5 MAPK10 RPS6KA2