Integration of Transcriptomic Profiling , Genome-wide Association , and Network Biology Reveals Molecular Mechanisms Underlying Blood Pressure Regulation

Tianxiao Huan, Qingying Meng, Mohamed A. Saleh, Allison E. Norlander, Roby Joehanes, Jun Zhu, Brian H. Chen, Bin Zhang, Andrew D. Johnson, Saixia Ying, Paul Courchesne, Nalini Raghavachari, Richard Wang, Poching Liu, The International Consortium for Blood Pressure GWAS (ICBP), Christopher J. O'Donnell, Ramachandran Vasan, Peter J. Munson, Meena S. Madhur, David G. Harrison, Xia Yang, and Daniel Levy

[1]  Jing Yang,et al.  The human disease network in terms of dysfunctional regulatory mechanisms , 2015, Biology Direct.

[2]  D. Levy,et al.  Lymphocyte adaptor protein LNK deficiency exacerbates hypertension and end-organ inflammation. , 2015, The Journal of clinical investigation.

[3]  B. Stranger,et al.  Expression QTL-based analyses reveal candidate causal genes and loci across five tumor types. , 2014, Human molecular genetics.

[4]  Akhilesh Pandey,et al.  Activation of diverse signaling pathways by oncogenic PIK3CA mutations , 2014, Nature Communications.

[5]  Ayellet V. Segrè,et al.  Integrative Genomics Reveals Novel Molecular Pathways and Gene Networks for Coronary Artery Disease , 2014, PLoS genetics.

[6]  T. Graeber,et al.  Complexity of metastasis-associated SDF-1 ligand signaling in breast cancer stem cells , 2014, Proceedings of the National Academy of Sciences.

[7]  P. Sullivan,et al.  Heritability and Genomics of Gene Expression in Peripheral Blood , 2014, Nature Genetics.

[8]  R. Taneja,et al.  Bhlhe40 controls cytokine production by T cells and is essential for pathogenicity in autoimmune neuroinflammation , 2014, Nature Communications.

[9]  A. Lusis,et al.  Systems genetics approaches to understand complex traits , 2013, Nature Reviews Genetics.

[10]  D. Koller,et al.  Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals , 2013, Genome research.

[11]  Hongyu Zhao,et al.  Integrating GWASs and human protein interaction networks identifies a gene subnetwork underlying alcohol dependence. , 2013, American journal of human genetics.

[12]  M. Peters,et al.  Systematic identification of trans eQTLs as putative drivers of known disease associations , 2013, Nature Genetics.

[13]  Pedro G. Ferreira,et al.  Transcriptome and genome sequencing uncovers functional variation in humans , 2013, Nature.

[14]  B. Tabakoff,et al.  Whole Brain and Brain Regional Coexpression Network Interactions Associated with Predisposition to Alcohol Consumption , 2013, PloS one.

[15]  Xia Yang,et al.  A Systems Biology Framework Identifies Molecular Underpinnings of Coronary Heart Disease , 2013, Arteriosclerosis, thrombosis, and vascular biology.

[16]  Andrew D. Johnson,et al.  Gene Expression Signatures of Coronary Heart Disease , 2013, Arteriosclerosis, thrombosis, and vascular biology.

[17]  S. Horvath,et al.  Genes and pathways underlying regional and cell type changes in Alzheimer's disease , 2013, Genome Medicine.

[18]  L. Tran,et al.  Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease , 2013, Cell.

[19]  Christie S. Chang,et al.  The BioGRID interaction database: 2013 update , 2012, Nucleic Acids Res..

[20]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..

[21]  B. Han,et al.  Human transcriptome analysis of acute responses to glucose ingestion reveals the role of leukocytes in hyperglycemia-induced inflammation. , 2012, Physiological genomics.

[22]  D. Granville,et al.  Granzyme B in injury, inflammation, and repair. , 2012, Trends in molecular medicine.

[23]  Steve Horvath,et al.  Systems analysis of primary Sjögren's syndrome pathogenesis in salivary glands identifies shared pathways in human and a mouse model , 2012, Arthritis Research & Therapy.

[24]  S. Horvath,et al.  Aging effects on DNA methylation modules in human brain and blood tissue , 2012, Genome Biology.

[25]  Yudong D. He,et al.  Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers , 2012, Molecular systems biology.

[26]  M. Jarvelin,et al.  Highly interconnected genes in disease-specific networks are enriched for disease-associated polymorphisms , 2012, Genome Biology.

[27]  H. Kobori,et al.  Interferon‐γ biphasically regulates angiotensinogen expression via a JAK‐STAT pathway and suppressor of cytokine signaling 1 (SOCS1) in renal proximal tubular cells , 2012, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[28]  Andrew G. Clark,et al.  Knowledge-Driven Analysis Identifies a Gene–Gene Interaction Affecting High-Density Lipoprotein Cholesterol Levels in Multi-Ethnic Populations , 2012, PLoS genetics.

[29]  Rafael C. Jimenez,et al.  The IntAct molecular interaction database in 2012 , 2011, Nucleic Acids Res..

[30]  Christian Gieger,et al.  Genetic Variants in Novel Pathways Influence Blood Pressure and Cardiovascular Disease Risk , 2011, Nature.

[31]  P. Aaronson,et al.  Key role of the RhoA/Rho kinase system in pulmonary hypertension. , 2011, Pulmonary pharmacology & therapeutics.

[32]  Antony Vinh,et al.  Inflammation, Immunity, and Hypertension , 2011, Hypertension.

[33]  Gary D. Bader,et al.  The Biomolecular Interaction Network Database in PSI-MI 2.5 , 2011, Database J. Biol. Databases Curation.

[34]  H. Kawamoto,et al.  The Role of the Basic Helix-Loop-Helix Transcription Factor Dec1 in the Regulatory T Cells , 2010, The Journal of Immunology.

[35]  G. Abecasis,et al.  MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes , 2010, Genetic epidemiology.

[36]  C. Farber,et al.  Identification of a gene module associated with BMD through the integration of network analysis and genome‐wide association data , 2010, Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research.

[37]  Y. Huang,et al.  A46G and C79G polymorphisms in the β2-adrenergic receptor gene (ADRB2) and essential hypertension risk: a meta-analysis , 2010, Hypertension Research.

[38]  P. Munroe,et al.  Common Variants in the ATP2B1 Gene Are Associated With Susceptibility to Hypertension: The Japanese Millennium Genome Project , 2010, Hypertension.

[39]  Xia Yang,et al.  Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver. , 2010, Genome research.

[40]  Toshihiro Tanaka,et al.  Regulatory polymorphism in transcription factor KLF5 at the MEF2 element alters the response to angiotensin II and is associated with human hypertension , 2010, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[41]  O. Carretero,et al.  Lack of Glutathione Peroxidase 1 Accelerates Cardiac-Specific Hypertrophy and Dysfunction in Angiotensin II Hypertension , 2010, Hypertension.

[42]  F. Faraci,et al.  Endogenous Interleukin-10 Inhibits Angiotensin II–Induced Vascular Dysfunction , 2009, Hypertension.

[43]  J. Oram,et al.  The cell cholesterol exporter ABCA1 as a protector from cardiovascular disease and diabetes. , 2009, Biochimica et biophysica acta.

[44]  Andrew D. Johnson,et al.  Genome-wide association study of blood pressure and hypertension , 2009, Nature Genetics.

[45]  J. Cogan,et al.  Penetrance of pulmonary arterial hypertension is modulated by the expression of normal BMPR2 allele , 2009, Human mutation.

[46]  Sandhya Rani,et al.  Human Protein Reference Database—2009 update , 2008, Nucleic Acids Res..

[47]  Steve Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[48]  John D. Storey,et al.  Mapping the Genetic Architecture of Gene Expression in Human Liver , 2008, PLoS biology.

[49]  S. Horvath,et al.  Variations in DNA elucidate molecular networks that cause disease , 2008, Nature.

[50]  Bin Zhang,et al.  Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R , 2008, Bioinform..

[51]  D. Geschwind,et al.  A Systems Level Analysis of Transcriptional Changes in Alzheimer's Disease and Normal Aging , 2008, The Journal of Neuroscience.

[52]  A. Barabasi,et al.  The human disease network , 2007, Proceedings of the National Academy of Sciences.

[53]  R. Knutsen,et al.  An afferent vagal nerve pathway links hepatic PPARalpha activation to glucocorticoid-induced insulin resistance and hypertension. , 2007, Cell metabolism.

[54]  Y. Kokubo,et al.  Association of Sixty-One Non-Synonymous Polymorphisms in Forty-One Hypertension Candidate Genes with Blood Pressure Variation and Hypertension , 2006, Hypertension Research.

[55]  S. Horvath,et al.  Evidence for anti-Burkitt tumour globulins in Burkitt tumour patients and healthy individuals. , 1967, British Journal of Cancer.

[56]  S. Mifflin,et al.  Increased c‐Fos in medullary cardiovascular nuclei in acute and chronic renal wrap hypertension , 2006 .

[57]  S. Horvath,et al.  A General Framework for Weighted Gene Co-Expression Network Analysis , 2005, Statistical applications in genetics and molecular biology.

[58]  J. Castle,et al.  An integrative genomics approach to infer causal associations between gene expression and disease , 2005, Nature Genetics.

[59]  R. Natarajan,et al.  Increased expression of cyclooxygenase-2 in human pancreatic islets treated with high glucose or ligands of the advanced glycation endproduct-specific receptor (AGER), and in islets from diabetic mice , 2005, Diabetologia.

[60]  A. Diehl Fatty liver, hypertension, and the metabolic syndrome , 2004, Gut.

[61]  Eoin Fahy,et al.  MitoProteome: mitochondrial protein sequence database and annotation system , 2004, Nucleic Acids Res..

[62]  R. Knutsen,et al.  Dexamethasone induction of hypertension and diabetes is PPAR-α dependent in LDL receptor–null mice , 2003, Nature Medicine.

[63]  John E Hall,et al.  The kidney, hypertension, and obesity. , 2003, Hypertension.

[64]  A. Marks Calcium and the heart: a question of life and death. , 2003, The Journal of clinical investigation.

[65]  R. Lifton,et al.  WNK1, a kinase mutated in inherited hypertension with hyperkalemia, localizes to diverse Cl−-transporting epithelia , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[66]  R. Trembath,et al.  Primary Pulmonary Hypertension Is Associated With Reduced Pulmonary Vascular Expression of Type II Bone Morphogenetic Protein Receptor , 2002, Circulation.

[67]  R. Flavell,et al.  Defective T cell activation and autoimmune disorder in Stra13-deficient mice , 2001, Nature Immunology.

[68]  C. Lindgren,et al.  Characterization of the annexin I gene and evaluation of its role in type 2 diabetes. , 2001, Diabetes.

[69]  B. Zinman,et al.  Association of a single nucleotide polymorphism in CPB2 encoding the thrombin-activable fibrinolysis inhibitor (TAF1) with blood pressure. , 2001, Clinical genetics.

[70]  R. Perlmutter,et al.  Control of B cell production by the adaptor protein lnk. Definition Of a conserved family of signal-modulating proteins. , 2000, Immunity.

[71]  L. Groop,et al.  A paired-sibling analysis of the XbaI polymorphism in the muscle glycogen synthase gene , 1999, Diabetologia.

[72]  J. Chalmers,et al.  Altered c-fos in rostral medulla and spinal cord of spontaneously hypertensive rats. , 1996, Hypertension.

[73]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[74]  L. Groop,et al.  Association between polymorphism of the glycogen synthase gene and non-insulin-dependent diabetes mellitus. , 1993, The New England journal of medicine.

[75]  C. Bouchard,et al.  Relationships between body fatness, adipose tissue distribution and blood pressure in men and women. , 1988, Journal of clinical epidemiology.

[76]  J. Whisnant,et al.  Hypertension and the Brain , 1974 .