Supplementary Table 1. Complete Diseases and Disorders results from IPA simulations.
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1 Supplementary Data Supplementary Table 1. Complete Diseases and Disorders results from IPA simulations. Disease/Disorder Percentage of Simulations in which Disease/Disorder was Significantly Associated with Data (p<0.05) Cancer 71 Developmental Disorder 50 Connective Tissue Disorder 37 Cardiovascular Disease 34 Neurological Disease 33 Gastrointestinal Disease 32 Dermatological Diseases and Conditions 21 Endocrine System Disorders 21 Skeletal and Muscular Disorders 21 Immunological Disease 20 Hereditary Disorder 19 Metabolic Disease 19 Hematological Disease 15 Inflammatory Response 13 Reproductive System Disease 13 Inflammatory Disease 11 Auditory Disease 10 Hepatic System Disease 10 Organismal Injury & Abnormalities 10 Genetic Disorder 9 Infectious Disease 9 Renal and Urological Disease 8 Respiratory Disease 6 Dental Disease 3 Opthalmic Disease 3 Psychological Disorders 2
2 Supplementary Table 2. Complete Molecular and Cellular results from IPA simulations. Percentage of Simulations in which was Significantly Associated with Data (p<0.05) Cellular Development 55 Cell Morphology 52 Cellular Assembly and Organization 45 Cell Death 36 Cell Cycle 34 Cellular Growth and Proliferation 31 Cell to Cell Signaling and Interaction 31 Cellular and Maintenance 29 Cellular Movement 23 Small Molecule Biochemistry 20 Molecular Transport 19 DN Replication, Recombination and Repair 17 Amino Acid Metabolism 14 Gene Expression 13 Cellular Compromise 13 Carbohydrate Metabolism 13 Lipid Metabolism 12 Post-Translational Modification 8 Drug Metabolism 8 Antigen Presentation 8 Nucleic Acid Metabolism 5 Cell Signaling 5 Protein Trafficking 2 Protein Synthesis 2 Energy Production 2 Vitamin and Mineral Metabolism 1 RNA Post-Transcriptional Modification 1 Free Radical Scavenging 1
3 Supplementary Table 3. Complete Physiological System Development and results from IPA simulations. Percentage of Simulations in which was Significantly Associated with Data (p<0.05) Embryonic Development 65 Tissue Development 41 Nervous System Development and 37 Organismal Development 35 Connective Tissue Development and 32 Organ Development 32 Organ Morphology 30 Tissue Morphology 27 Hematological System Development and 26 Cardiovascular System Development and 23 Skeletal and Muscular System 22 Development and Hematopoiesis 17 Reproductive System Development and 17 Digestive System Development and 16 Behavior 14 Lymphoid Tissue Structure and 12 Development Endocrine System Development and 9 Cell-Mediated Immune Response 8 Renal and Urological System Development 8 and Hair and Skin Development and 6 Respiratory System Development and 5 Auditory and Vestibular System 4 Development and Immune Cell Trafficking 4 Humoral Immune Response 3 Visual System Development and 3 Organismal s 2 Hepatic System Development and 1
4 Tumor Morphology 1
5 Supplementary Table 4. Complete Top Canonical Pathways results from IPA simulations. Pathway Percentage of Simulations in which was Significantly Associated with Data (p<0.05) Axonal Guidance Signaling 6 Calcium Signaling 6 Clathrin-Mediated Endocytosis Signaling 6 Cyclins and Cell Cycle Regulation 6 Glioblastoma Multiforme Signaling 6 Aryl Hydrocarbon Receptor Signaling 5 Cardiac β-adrenergic Signaling 5 Cell Cycle: G1/S Checkpoint Regulation 5 Ephrin B signaling 5 ERK/MAPK signaling 5 IL-4 Signaling 5 Protein Ubiquitination Pathway 5 Antigen Presentation Pathway 4 Chronic Myeloid Leukemia Signaling 4 ERK5 signaling 4 Glioma Signaling 4 Huntington's Disease Signaling 4 Netrin Signaling 4 Role of WNT/GSK-3β Signaling in the 4 Pathogenesis of Influenza Tyrosine Metabolism 4 Valine, Leucine and Isoleucine 4 Degradation Wnt/β-Catenin Signaling 4 α-adrenergic Signaling 3 Amyloid Processing 3 Assembly of RNA Polymerase III Complex 3 Basal Cell Carcinoma Signaling 3 Caveolar-Mediated Endocytosis Signaling 4 CD27 Signaling in Lymphocytes 3 CDC42 signaling 3 Dopamine Receptor Signaling 3 Ephrin Receptor Signaling 3 Embryonic Stem Cell Differentiation Into 3 Cardiac Lineages Estrogen Receptor Signaling 3 Glutamate Receptor Signaling 3 HER2 Signaling in Breast Cancer 3 Keratan Sulfate Biosynthesis 3
6 Melanocyte Development and 3 Pigmentation Signaling MSP-RON Signaling Pathway 3 Neuroprotective Role of THOP1 in 3 Alzheimer's Disease NF-κB Signaling 3 Nucleotide Excision Repair Pathway 3 nnos Signaling in Neurons 3 p53 Signaling 3 PPAR Signaling 3 pten Signaling 3 rhogdi Signaling 3 Role of BRCA1 in DNA Damage 3 Response Role of CHK Proteins in Cell Cycle 3 Checkpoint Control Role of Oct4 in Mammalian Embryonic 3 Stem Cell Pluripotency Role of NANOG in Mammalian 3 Embryonic Stem Cell Pluripotency Role of Tissue Factor in Cancer 3 Starch and Sucrose Metabolism 3 Telomerase Signaling 3 Transcriptional Regulatory Network in 3 Embryonic Stem Cells TR/RXR Activation 3 4-1BB Signaling in T Lymphocytes 2 Agrin Interactions at Neuromuscular 2 Junction Airway Pathology in Chronic Obstructive 2 Pulmonary Disease Acute Phase Response Signaling 2 AMPK Signaling 2 B-Cell Activating Factor Signaling 2 Breast Cancer Regulation by Stathmin1 2 Calcium-Induced T Lymphocyte Apoptosis 2 camp-mediated Signaling 2 CCR5 Signaling in Macrophages 2 CD40 signaling 2 Corticotropin Releasing Hormone 2 Signaling CREB Signaling in Neurons 2 Dopamine-DARPP32 Feedback in camp 2 Signaling DNA Double-Strand Break Repair by Non- 2
7 Homologous End Joining DNA Methylation and Transcriptional 2 Repression Signaling Factors Promoting Cardiogenesis in 2 Vertebrates G-Protein Coupled Receptor Signaling 2 G-Protein Signaling Mediated by Tubby 2 Graft-versus-Host Disease Signaling 2 Hematopoiesis From Pluripotent Stem 2 Cells HGF Signaling 2 Histidine Metabolism 2 Human Embryonic Stem Cell Pluripotency 2 IL-3 Signaling 2 Induction of Apoptosis by HIV-1 2 Lysine Biosynthesis 2 Lysine Degradation 2 Molecular Mechanisms of Cancer 2 mtor Signaling 2 N-Glycan Biosynthesis 2 NF-κB Activation by Viruses 2 Nitric Acid Signaling in the Cardiovascular 2 System PAK signaling 2 Pentose and Glucoronate Interconversions 2 Primary Immunodeficiency Signaling 2 Propanoate Metabolism 2 Purine Metabolism 2 PXR/RXR Activation 2 Pyrimidine Metabolism 2 Pyruvate Metabolism 2 RAR Activation 2 Retinol Metabolism 2 Role of IL-17 in Allergic Inflammatory 2 Airway Diseases Role of IL-17A in Psoriasis 2 Role of Macrophages, Fibroblasts, and 2 Endothelial Cells in Rheumatoid Arthritis Role of Osteoblasts, Osteoclasts and 2 Chondrocytes in Rheumatoid Arthritis Role of NFAT in Cardiac Hypertrophy 2 Selenomamino Acid Metabolism 2 Semaphorin Signaling in Neurons 2 Small Cell Lung Cancer Signaling 2 TGF-β Signaling 2
8 Tight Junction Signaling 2 Thrombin Signaling 2 Thrombopoietin Signaling 2 Toll-Like Receptor Signaling 2 TNFR1 Signaling 2 Tryptophan Metabolism 2 Type I Diabetes Mellitus Signaling 2 VDR/RXR Activation Mediated Signaling 1 Airway Inflammation in Asthma 1 Activation of IRF by Cytosolic Pattern 1 Recognition Receptors Acute Myeloid Leukemia Signaling 1 Aminoacyl-tRNA Biosynthesis 1 Aminosugars Metabolism 1 Androgen Signaling 1 Androgen and Estrogen Metabolism 1 Angiopoietin Signaling 1 Antiproliferative Role of Somatostatin 1 Receptor 2 Arachidonic Acid Metabolism 1 Ascorbate and Aldarate Metabolism 1 Assembly of RNA Polymerase I Complex 1 Assembly of RNA Polymerase II Complex 1 Atherosclerosis Signaling 1 ATM Signaling 1 Autoimmune Thyroid Disease Signaling 1 β-alanine Metabolism 1 Bile Acid Biosynthesis 1 Bladder Cancer Signaling 1 Butanoate Metabolism 1 Cardiac Hypertrophy Signaling 1 CD28 Signaling in T Helper Cells 1 CDK5 Signaling 1 Cell Cycle: G2/M DNA Damage 1 Checkpoint Regulation Cellular Effects of Sildenafil (Viagra) 1 Chondroitin Sulfate Biosynthesis 1 Circadian Rhythm Signaling 1 Cleavage and Polyadenylation of premrna 1 CNTF Signaling 1 Coagulation System 1 Complement System 1 Cysteine Metabolism 1
9 D-Glutamine and D-Glutamate metabolism 1 Death Receptor Signaling 1 DNA Double-Strand Break Repair by 1 Homologous Recombination EGF Signaling 1 enos Signaling 1 Endometrial Cancer Signaling 1 Extrinsic Prothrombin Activation Pathway 1 FAK Signaling 1 Fatty Acid Biosynthesis 1 Fatty Acid Elongation in Mitochondria 1 fcgriib signaling in B lymphocytes 1 fmlp signaling in neutrophils 1 G Beta Gamma Signaling 1 GABA Receptor Signaling 1 Germ Cell-Sertoli Cell Junction Signaling 1 Glycerolipid Metabolism 1 GM-CSF Signaling 1 GnRH Signaling 1 Growth Hormone Signaling 1 Hepatic Fibrosis/Hepatic Stellate Cell 1 Activation Hereditary Breast Cancer Signaling 1 HMGB1 Signaling 1 Hypoxia Signaling in the Cardiovascular 1 System icos-icosl Signaling in T-Helper Cells 1 IL-8 Signaling 1 Inositol Phosphate Metabolism 1 Insulin Receptor Signaling 1 Integrin Signaling 1 Intrinsic Prothrombin Activation Pathway 1 JAK/STAT Signaling 1 Linoleic Acid Metabolism 1 Lymphotoxin β Receptor Signaling 1 Macropinocytosis Signaling 1 Melatonin Signaling 1 MIF-Mediated Glucocorticoid Regulation 1 MIF Regulation of Innate Immunity 1 Mismatch Repair in Eukaryotes 1 Mitotic Roles of Polo-like Kinase 1 Mouse Embryonic Stem Cell Pluripotency 1 Neuregulin Signaling 1 Nicotinate and Nicotinamide Metabolism 1 Nitric Oxide Signaling in the 1
10 Cardiovascular System Neuregulin Signaling 1 Non-Small Cell Lung Cancer Signaling 1 Notch Signaling 1 Oncostatin M Signaling 1 Oxidative Phosphorylation 1 p13k Signaling in B Lymphocytes 1 p13/akt Signaling 1 P2Y Purigenic Receptor Signaling Pathway 1 p38 MAPK Signaling 1 Phenylalanine Metabolism 1 Phospholipid Degradation 1 Phototransduction Pathway 1 PKC Theta Signaling in T Lymphocytes 1 Prostate Cancer Signaling 1 Protein Kinase A Signaling 1 Regulation of IL-2 Expression in Activated 1 and Anergic T Lymphocytes Relaxin Signaling 1 Renin-Angiotensis Signaling 1 rhoa Signaling 1 Role of p13/akt Signaling in the 1 Pathogenesis of Influenza Role of PKR in Interferon Induction and 1 Antiviral Response Role of RIG1-like Receptors in Antiviral 1 Innate Immunity Signaling by Rho Family GTPases 1 Sphingolipid Metabolism 1 Synaptic Long Term Depression 1 Synaptic Long Term Potentiation 1 T Helper Cell Differentiation 1 Taurine and Hypotaurine Metabolism 1 Telomere Extension by Telomerase 1 Virus Entry via Endocytic Pathways 1 Xenobiotic Metabolism Signaling 1
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12 Supplementary Figure 2. The distribution of correlations between β values in samples from a single chip in Run One and the corresponding samples from Run Two. Histograms show the pre-combat distribution of Spearman s correlations between nonrandomized Run One and randomized Run Two for A) Chip 1; B) Chip 2; C) Chip 3; D) Chip 4.
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