Variations in DNA elucidate molecular networks that cause disease (original) (raw)

• Edwards, A. O. et al. Complement factor H polymorphism and age-related macular degeneration. Science 308, 421–424 (2005)
  Article ADS CAS Google Scholar
• Haines, J. L. et al. Complement factor H variant increases the risk of age-related macular degeneration. Science 308, 419–421 (2005)
  Article ADS CAS Google Scholar
• Klein, R. J. et al. Complement factor H polymorphism in age-related macular degeneration. Science 308, 385–389 (2005)
  Article ADS CAS Google Scholar
• Sladek, R. et al. A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 445, 881–885 (2007)
  Article ADS CAS Google Scholar
• Frayling, T. M. et al. A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity. Science 316, 889–894 (2007)
  Article ADS CAS Google Scholar
• Strittmatter, W. J. et al. Apolipoprotein E: high-avidity binding to β-amyloid and increased frequency of type 4 allele in late-onset familial Alzheimer disease. Proc. Natl Acad. Sci. USA 90, 1977–1981 (1993)
  Article ADS CAS Google Scholar
• Brem, R. B., Yvert, G., Clinton, R. & Kruglyak, L. Genetic dissection of transcriptional regulation in budding yeast. Science 296, 752–755 (2002)
  Article ADS CAS Google Scholar
• Bystrykh, L. et al. Uncovering regulatory pathways that affect hematopoietic stem cell function using ‘genetical genomics’. Nature Genet. 37, 225–232 (2005)
  Article CAS Google Scholar
• Chesler, E. J. et al. Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nature Genet. 37, 233–242 (2005)
  Article CAS Google Scholar
• Monks, S. A. et al. Genetic inheritance of gene expression in human cell lines. Am. J. Hum. Genet. 75, 1094–1105 (2004)
  Article CAS Google Scholar
• Schadt, E. E. et al. An integrative genomics approach to infer causal associations between gene expression and disease. Nature Genet. 37, 710–717 (2005)
  Article CAS Google Scholar
• Schadt, E. E. et al. Genetics of gene expression surveyed in maize, mouse and man. Nature 422, 297–302 (2003)
  Article ADS CAS Google Scholar
• Hartwell, L. H., Hopfield, J. J., Leibler, S. & Murray, A. W. From molecular to modular cell biology. Nature 402, C47–C52 (1999)
  Article CAS Google Scholar
• Schadt, E. E., Sachs, A. & Friend, S. Embracing complexity, inching closer to reality. Sci. STKE 2005, pe40 (2005)
  PubMed Google Scholar
• Paigen, B., Albee, D., Holmes, P. A. & Mitchell, D. Genetic analysis of murine strains C57BL/6J and C3H/HeJ to confirm the map position of Ath-1, a gene determining atherosclerosis susceptibility. Biochem. Genet. 25, 501–511 (1987)
  Article CAS Google Scholar
• Yang, X. et al. Tissue-specific expression and regulation of sexually dimorphic genes in mice. Genome Res. 16, 995–1004 (2006)
  Article CAS Google Scholar
• Wang, S. et al. Genetic and genomic analysis of a fat mass trait with complex inheritance reveals marked sex specificity. PLoS Genet. 2, e15 (2006)
  Article Google Scholar
• Paigen, B. et al. Ath-1, a gene determining atherosclerosis susceptibility and high density lipoprotein levels in mice. Proc. Natl Acad. Sci. USA 84, 3763–3767 (1987)
  Article ADS CAS Google Scholar
• Castellani, L. W., Goto, A. M. & Lusis, A. J. Studies with apolipoprotein A-II transgenic mice indicate a role for HDLs in adiposity and insulin resistance. Diabetes 50, 643–651 (2001)
  Article CAS Google Scholar
• Wang, X., Korstanje, R., Higgins, D. & Paigen, B. Haplotype analysis in multiple crosses to identify a QTL gene. Genome Res. 14, 1767–1772 (2004)
  Article CAS Google Scholar
• Wang, X. et al. Positional identification of TNFSF4, encoding OX40 ligand, as a gene that influences atherosclerosis susceptibility. Nature Genet. 37, 365–372 (2005)
  Article CAS Google Scholar
• Warden, C. H., Hedrick, C. C., Qiao, J. H., Castellani, L. W. & Lusis, A. J. Atherosclerosis in transgenic mice overexpressing apolipoprotein A-II. Science 261, 469–472 (1993)
  Article ADS CAS Google Scholar
• Welch, C. L. et al. Novel QTLs for HDL levels identified in mice by controlling for Apoa2 allelic effects: confirmation of a chromosome 6 locus in a congenic strain. Physiol. Genomics 17, 48–59 (2004)
  Article CAS Google Scholar
• Doolittle, M. H., LeBoeuf, R. C., Warden, C. H., Bee, L. M. & Lusis, A. J. A polymorphism affecting apolipoprotein A-II translational efficiency determines high density lipoprotein size and composition. J. Biol. Chem. 265, 16380–16388 (1990)
  CAS PubMed Google Scholar
• Pajukanta, P. et al. Familial combined hyperlipidemia is associated with upstream transcription factor 1 (USF1). Nature Genet. 36, 371–376 (2004)
  Article CAS Google Scholar
• Babinska, A. et al. F11-receptor (F11R/JAM) mediates platelet adhesion to endothelial cells: role in inflammatory thrombosis. Thromb. Haemost. 88, 843–850 (2002)
  Article Google Scholar
• Huertas-Vazquez, A. et al. Familial combined hyperlipidemia in Mexicans: association with upstream transcription factor 1 and linkage on chromosome 16q24.1. Arterioscler. Thromb. Vasc. Biol. 25, 1985–1991 (2005)
  Article CAS Google Scholar
• Ezzahiri, R. et al. Chlamydia pneumoniae infections augment atherosclerotic lesion formation: a role for serum amyloid P. APMIS 114, 117–126 (2006)
  Article CAS Google Scholar
• Adams, L. D., Geary, R. L., Li, J., Rossini, A. & Schwartz, S. M. Expression profiling identifies smooth muscle cell diversity within human intima and plaque fibrous cap: loss of RGS5 distinguishes the cap. Arterioscler. Thromb. Vasc. Biol. 26, 319–325 (2006)
  Article CAS Google Scholar
• Chang, Y. P. et al. Multiple genes for essential-hypertension susceptibility on chromosome 1q. Am. J. Hum. Genet. 80, 253–264 (2007)
  Article CAS Google Scholar
• Mehrabian, M. et al. Integrating genotypic and expression data in a segregating mouse population to identify 5-lipoxygenase as a susceptibility gene for obesity and bone traits. Nature Genet. 37, 1224–1233 (2005)
  Article CAS Google Scholar
• Austyn, J. M. & Gordon, S. F4/80, a monoclonal antibody directed specifically against the mouse macrophage. Eur. J. Immunol. 11, 805–815 (1981)
  Article CAS Google Scholar
• Ramprasad, M. P., Terpstra, V., Kondratenko, N., Quehenberger, O. & Steinberg, D. Cell surface expression of mouse macrosialin and human CD68 and their role as macrophage receptors for oxidized low density lipoprotein. Proc. Natl Acad. Sci. USA 93, 14833–14838 (1996)
  Article ADS CAS Google Scholar
• Wright, S. D., Ramos, R. A., Tobias, P. S., Ulevitch, R. J. & Mathison, J. C. CD14, a receptor for complexes of lipopolysaccharide (LPS) and LPS binding protein. Science 249, 1431–1433 (1990)
  Article ADS CAS Google Scholar
• Kubota, N. et al. PPARγ mediates high-fat diet-induced adipocyte hypertrophy and insulin resistance. Mol. Cell 4, 597–609 (1999)
  Article CAS Google Scholar
• Hu, Y., Liu, W., Huang, R. & Zhang, X. A systematic review and meta-analysis of the relationship between lipoprotein lipase Asn291Ser variant and diseases. J. Lipid Res. 47, 1908–1914 (2006)
  Article CAS Google Scholar
• Preiss-Landl, K., Zimmermann, R., Hammerle, G. & Zechner, R. Lipoprotein lipase: the regulation of tissue specific expression and its role in lipid and energy metabolism. Curr. Opin. Lipidol. 13, 471–481 (2002)
  Article CAS Google Scholar
• Yost, T. J., Jensen, D. R. & Eckel, R. H. Tissue-specific lipoprotein lipase: relationships to body composition and body fat distribution in normal weight humans. Obes. Res. 1, 1–4 (1993)
  Article CAS Google Scholar
• Liobikas, J. et al. Expression and purification of the mitochondrial serine protease LACTB as an N-terminal GST fusion protein in Escherichia coli. Protein Expr. Purif. 45, 335–342 (2006)
  Article CAS Google Scholar
• Smith, T. S. et al. Identification, genomic organization, and mRNA expression of LACTB, encoding a serine β-lactamase-like protein with an amino-terminal transmembrane domain. Genomics 78, 12–14 (2001)
  Article CAS Google Scholar
• Jacobs, C. Life in the balance: cell walls and antibiotic resistance. Science 278, 1731–1732 (1997)
  Article ADS CAS Google Scholar
• Gaucher, S. P. et al. Expanded coverage of the human heart mitochondrial proteome using multidimensional liquid chromatography coupled with tandem mass spectrometry. J. Proteome Res. 3, 495–505 (2004)
  Article CAS Google Scholar
• Mootha, V. K. et al. Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell 115, 629–640 (2003)
  Article CAS Google Scholar
• Taylor, S. W. et al. Characterization of the human heart mitochondrial proteome. Nature Biotechnol. 21, 281–286 (2003)
  Article CAS Google Scholar
• Bains, R. K. et al. Visceral obesity without insulin resistance in late-onset obesity rats. Endocrinology 145, 2666–2679 (2004)
  Article CAS Google Scholar
• Schadt, E. E. & Lum, P. Y. Reverse engineering gene networks to identify key drivers of complex disease phenotypes. J. Lipid Res. 47, 2601–2013 (2006)
  Article CAS Google Scholar
• Lum, P. Y. et al. Elucidating the murine brain transcriptional network in a segregating mouse population to identify core functional modules for obesity and diabetes. J. Neurochem. 97, (suppl. 1)50–62 (2006)
  Article CAS Google Scholar
• Ravasz, E., Somera, A. L., Mongru, D. A., Oltvai, Z. N. & Barabasi, A. L. Hierarchical organization of modularity in metabolic networks. Science 297, 1551–1555 (2002)
  Article ADS CAS Google Scholar
• Haley, C. S. & Knott, S. A. A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69, 315–324 (1992)
  Article CAS Google Scholar
• Jiang, C. & Zeng, Z. B. Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics 140, 1111–1127 (1995)
  CAS PubMed PubMed Central Google Scholar