1 S4 Table. Overlapped KEGG pathways with large transcript network ...

1 KEGG Pathway Long-term potentiation Fc epsilon RI signaling pathway Fc gamma R-mediated phagocytosis Axon guidance VEGF signaling pathway GnRH signaling pathway Phosphatidylinositol signaling system ErbB signaling pathway Inositol phosphate metabolism Neuroactive ligand-receptor interaction Glycerophospholipid metabolism Olfactory transduction Neurotrophin signaling pathway Central carbon metabolism in cancer Natural killer cell mediated cytotoxicity Glutamatergic synapse Retrograde endocannabinoid signaling RNA polymerase Glioma Ras signaling pathway Inflammatory mediator regulation of TRP channels Long-term depression Gap junction B cell receptor signaling pathway Tight junction Glycerolipid metabolism mTOR signaling pathway T cell receptor signaling pathway Vascular smooth muscle contraction Non-small cell lung cancer Chemokine signaling pathway Cell adhesion molecules (CAMs) Choline metabolism in cancer MAPK signaling pathway Epithelial cell signaling in Helicobacter pylori infection Oxytocin signaling pathway Type II diabetes mellitus Adherens junction Lysine degradation Circadian entrainment Prolactin signaling pathway Insulin signaling pathway Cholinergic synapse Morphine addiction Bladder cancer Platelet activation Progesterone-mediated oocyte maturation Toll-like receptor signaling pathway Rap1 signaling pathway Leukocyte transendothelial migration Pancreatic cancer Complement and coagulation cascades Acute myeloid leukemia Renal cell carcinoma Endometrial cancer Sphingolipid signaling pathway Focal adhesion Regulation of actin cytoskeleton FoxO signaling pathway Amyotrophic lateral sclerosis (ALS) Osteoclast differentiation Melanoma Serotonergic synapse Gastric acid secretion Hepatitis C Dopaminergic synapse Calcium signaling pathway Pathogenic Escherichia coli infection Influenza A Estrogen signaling pathway Chronic myeloid leukemia Aldosterone-regulated sodium reabsorption Ovarian steroidogenesis NOD-like receptor signaling pathway cAMP signaling pathway Colorectal cancer Proteoglycans in cancer Prostate cancer RIG-I-like receptor signaling pathway Signaling pathways regulating pluripotency of stem cells cGMP-PKG signaling pathway Thyroid hormone signaling pathway TGF-beta signaling pathway Endocytosis ECM-receptor interaction Adipocytokine signaling pathway Hepatitis B Jak-STAT signaling pathway HIF-1 signaling pathway Glucagon signaling pathway Ubiquitin mediated proteolysis TNF signaling pathway PI3K-Akt signaling pathway AMPK signaling pathway Wnt signaling pathway Adrenergic signaling in cardiomyocytes NF-kappa B signaling pathway MicroRNAs in cancer Cell cycle Pathways in cancer

# of gene in KEGG 67 70 91 127 61 92 82 87 63 275 95 407 120 67 134 116 103 32 65 228 99 60 89 72 138 59 60 104 121 56 189 142 101 257 68 159 48 73 52 97 72 140 113 93 38 131 88 106 211 118 66 69 57 66 52 120 207 215 134 51 131 71 114 75 133 131 180 55 175 100 73 39 51 57 200 62 204 89 70 142 167 119 80 213 87 70 146 156 103 102 137 110 347 124 140 149 91 297 124 398

# of overlapped gene 30 51 45 56 39 53 26 70 14 38 12 15 88 38 47 21 25 11 46 119 45 25 42 45 49 13 35 80 43 45 86 32 56 156 36 63 23 48 11 28 52 75 42 21 34 57 63 56 119 51 58 23 48 55 41 66 103 95 94 20 82 50 29 24 73 44 51 22 76 51 63 22 18 31 82 52 130 70 35 84 56 62 51 84 23 38 98 69 68 33 66 79 166 59 76 62 55 109 91 260

Interactions 552 1426 1002 1526 736 1356 318 2272 86 626 62 92 3128 580 848 168 238 46 800 5182 722 220 620 706 830 58 418 2178 622 662 2408 332 1012 7830 414 1264 166 722 36 232 792 1634 512 126 322 892 1074 842 3722 680 870 136 586 754 414 1068 2600 2210 2102 94 1544 566 190 130 1194 426 570 104 1172 524 796 96 64 186 1298 498 3082 884 220 1250 542 662 446 1204 90 242 1510 734 710 166 654 894 3904 476 774 496 380 1484 734 5702

Density 61.33% 54.83% 49.48% 48.66% 48.39% 48.27% 47.04% 46.37% 43.88% 43.35% 43.06% 40.89% 40.39% 40.17% 38.39% 38.10% 38.08% 38.02% 37.81% 36.59% 35.65% 35.20% 35.15% 34.86% 34.57% 34.32% 34.12% 34.03% 33.64% 32.69% 32.56% 32.42% 32.27% 32.17% 31.94% 31.85% 31.38% 31.34% 29.75% 29.59% 29.29% 29.05% 29.02% 28.57% 27.85% 27.45% 27.06% 26.85% 26.28% 26.14% 25.86% 25.71% 25.43% 24.93% 24.63% 24.52% 24.51% 24.49% 23.79% 23.50% 22.96% 22.64% 22.59% 22.57% 22.41% 22.00% 21.91% 21.49% 20.29% 20.15% 20.06% 19.83% 19.75% 19.35% 19.30% 18.42% 18.24% 18.04% 17.96% 17.72% 17.28% 17.22% 17.15% 17.06% 17.01% 16.76% 15.72% 15.42% 15.35% 15.24% 15.01% 14.32% 14.17% 13.67% 13.40% 12.90% 12.56% 12.49% 8.86% 8.43%

S4 Table. Overlapped KEGG pathways with large transcript network. We consider the subnetwork of genes that are members of one KEGG pathway and calculated the density of DDIs in the subnetwork.