Erratum: Genetic Architecture of Atherosclerosis in Mice: A Systems Genetics Analysis of Common Inbred Strains (PLoS Genet (2015) 11:12 (e1005711) DOI: 10.1371/journal.pgen.1005711);Genetic Architecture of Atherosclerosis in Mice: A Systems Genetics Analysis of Common Inbred Strains

PLoS Genetics

Volumn 11, Issue 12, 2015, Pages

  Bennett, Brian J ^a,e   Davis, Richard C ^a   Civelek, Mete ^a   Orozco, Luz ^a   Wu, Judy ^a   Qi, Hannah ^a   Pan, Calvin ^a   Packard, René R Sevag ^a   Eskin, Eleazar ^b   Yan, Mujing ^c   Kirchgessner, Todd ^c   Wang, Zeneng ^d   Li, Xinmin ^d   Gregory, Jill C ^d   Hazen, Stanley L ^d   Gargalovic, Peter S ^c   Lusis, Aldons J ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of California   (United States)

^c BRISTOL MYERS SQUIBB   (United States)

^d LERNER RESEARCH INSTITUTE   (United States)

^e UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APOLIPOPROTEIN E; ARGININE; CHOLESTEROL ESTER TRANSFER PROTEIN; CYTOKINE; GLUCOSE; INSULIN; LIPID; LOW DENSITY LIPOPROTEIN CHOLESTEROL; TRIMETHYLAMINE OXIDE; VERY LOW DENSITY LIPOPROTEIN CHOLESTEROL; CETP PROTEIN, HUMAN; METHYLAMINE; TRANSCRIPTOME; TRIMETHYLOXAMINE;

ANIMAL EXPERIMENT; AORTA; ARTICLE; ATHEROSCLEROSIS; CONTROLLED STUDY; CORONARY ARTERY DISEASE; ENVIRONMENTAL FACTOR; FEMALE; GENE EXPRESSION; GENE INTERACTION; GENE LOCUS; GENE MAPPING; GENETIC ANALYSIS; GENETIC ASSOCIATION; GLUCOSE BLOOD LEVEL; HEREDITY; INBRED MOUSE STRAIN; INSULIN BLOOD LEVEL; LIPID BLOOD LEVEL; LIVER; MACROPHAGE; METABOLITE; MOUSE; NONHUMAN; PROTEIN EXPRESSION; RISK FACTOR; ANIMAL; BLOOD; C57BL MOUSE; GENETICS; HUMAN; INBREEDING; METABOLISM; PATHOLOGY; QUANTITATIVE TRAIT LOCUS;

ANIMALS; AORTA; APOLIPOPROTEINS E; ATHEROSCLEROSIS; CHOLESTEROL ESTER TRANSFER PROTEINS; CHOLESTEROL, LDL; HUMANS; INBREEDING; INSULIN; MACROPHAGES; METHYLAMINES; MICE; MICE, INBRED C57BL; QUANTITATIVE TRAIT LOCI; TRANSCRIPTOME;

EID: 84953295344     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/JOURNAL.PGEN.1005913     Document Type: Erratum

References (118)

1. Go AS, Mozaffarian D, Roger VL, Benjamin EJ, Berry JD, Borden WB, et al. Heart disease and stroke statistics—2013 update: a report from the American Heart Association. Circulation. 2013;127(1):e6–e245. Epub 2012/12/15. doi: 10.1161/CIR.0b013e31828124ad 23239837
2. Kathiresan S, Srivastava D, Genetics of human cardiovascular disease. Cell. 2012;148(6):1242–57. Epub 2012/03/20. doi: 10.1016/j.cell.2012.03.001 22424232
3. Lusis AJ, Genetics of atherosclerosis. Trends Genet. 2012;28(6):267–75. Epub 2012/04/07. doi: 10.1016/j.tig.2012.03.001 22480919
4. Stylianou IM, Bauer RC, Reilly MP, Rader DJ, Genetic basis of atherosclerosis: insights from mice and humans. Circ Res. 2012;110(2):337–55. Epub 2012/01/24. doi: 10.1161/CIRCRESAHA.110.230854 22267839
5. Deloukas P, Kanoni S, Willenborg C, Farrall M, Assimes TL, Thompson JR, et al. Large-scale association analysis identifies new risk loci for coronary artery disease. Nat Genet. 2013;45(1):25–33. Epub 2012/12/04. doi: 10.1038/ng.2480 23202125
6. Willer CJ, Schmidt EM, Sengupta S, Peloso GM, Gustafsson S, Kanoni S, et al. Discovery and refinement of loci associated with lipid levels. Nat Genet. 2013;45(11):1274–83. Epub 2013/10/08. doi: 10.1038/ng.2797 24097068
7. Musunuru K, Strong A, Frank-Kamenetsky M, Lee NE, Ahfeldt T, Sachs KV, et al. From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus. Nature. 2010;466(7307):714–9. Epub 2010/08/06. doi: 10.1038/nature09266 20686566
8. Erdmann J, Stark K, Esslinger UB, Rumpf PM, Koesling D, de Wit C, et al. Dysfunctional nitric oxide signalling increases risk of myocardial infarction. Nature. 2013;504(7480):432–6. Epub 2013/11/12. doi: 10.1038/nature12722 24213632
9. Zuk O, Schaffner SF, Samocha K, Do R, Hechter E, Kathiresan S, et al. Searching for missing heritability: designing rare variant association studies. Proc Natl Acad Sci U S A. 2014;111(4):E455–64. doi: 10.1073/pnas.1322563111 24443550
10. Civelek M, Lusis AJ, Systems genetics approaches to understand complex traits. Nat Rev Genet. 2014;15(1):34–48. Epub 2013/12/04. doi: 10.1038/nrg3575 24296534
11. Flint J, Eskin E, Genome-wide association studies in mice. Nat Rev Genet. 2012;13(11):807–17. Epub 2012/10/10. doi: 10.1038/nrg3335 23044826
12. Bennett BJ, Farber CR, Orozco L, Kang HM, Ghazalpour A, Siemers N, et al. A high-resolution association mapping panel for the dissection of complex traits in mice. Genome Res. 2010;20(2):281–90. Epub 2010/01/08. doi: 10.1101/gr.099234.109 20054062
13. Farber CR, Bennett BJ, Orozco L, Zou W, Lira A, Kostem E, et al. Mouse genome-wide association and systems genetics identify Asxl2 as a regulator of bone mineral density and osteoclastogenesis. PLoS Genet. 2011;7(4):e1002038. Epub 2011/04/15. doi: 10.1371/journal.pgen.1002038 21490954
14. Orozco LD, Bennett BJ, Farber CR, Ghazalpour A, Pan C, Che N, et al. Unraveling Inflammatory Responses using Systems Genetics and Gene-Environment Interactions in Macrophages. Cell. 2012;151(3):658–70. Epub 2012/10/30. doi: 10.1016/j.cell.2012.08.043 23101632
15. Parks BW, Nam E, Org E, Kostem E, Norheim F, Hui ST, et al. Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice. Cell Metab. 2013;17(1):141–52. Epub 2013/01/15. doi: 10.1016/j.cmet.2012.12.007 23312289
16. Rau CD, Lusis AJ, Wang Y, Genetics of common forms of heart failure: challenges and potential solutions. Current opinion in cardiology. 2015;30(3):222–7. Epub 2015/03/15. doi: 10.1097/HCO.0000000000000160 25768955
17. Parks BW, Sallam T, Mehrabian M, Psychogios N, Hui ST, Norheim F, et al. Genetic architecture of insulin resistance in the mouse. Cell Metab. 2015;21(2):334–46. Epub 2015/02/05. doi: 10.1016/j.cmet.2015.01.002 25651185
18. Plump AS, Smith JD, Hayek T, Aalto-Setala K, Walsh A, Verstuyft JG, et al. Severe hypercholesterolemia and atherosclerosis in apolipoprotein E-deficient mice created by homologous recombination in ES cells. Cell. 1992;71(2):343–53. 1423598
19. Zhang SH, Reddick RL, Piedrahita JA, Maeda N, Spontaneous hypercholesterolemia and arterial lesions in mice lacking apolipoprotein E. Science. 1992;258(5081):468–71. 1411543
20. Ishibashi S, Brown MS, Goldstein JL, Gerard RD, Hammer RE, Herz J, Hypercholesterolemia in low density lipoprotein receptor knockout mice and its reversal by adenovirus-mediated gene delivery. J Clin Invest. 1993;92(2):883–93. Epub 1993/08/01. 8349823
21. Lutgens E, Daemen M, Kockx M, Doevendans P, Hofker M, Havekes L, et al. Atherosclerosis in APOE*3-Leiden transgenic mice: from proliferative to atheromatous stage. Circulation. 1999;99(2):276–83. Epub 1999/01/20. 9892595
22. Westerterp M, van der Hoogt CC, de Haan W, Offerman EH, Dallinga-Thie GM, Jukema JW, et al. Cholesteryl ester transfer protein decreases high-density lipoprotein and severely aggravates atherosclerosis in APOE*3-Leiden mice. Arterioscler Thromb Vasc Biol. 2006;26(11):2552–9. Epub 2006/09/02. 16946130
23. Barajas B, Che N, Yin F, Rowshanrad A, Orozco LD, Gong KW, et al. NF-E2-related factor 2 promotes atherosclerosis by effects on plasma lipoproteins and cholesterol transport that overshadow antioxidant protection. Arterioscler Thromb Vasc Biol. 2011;31(1):58–66. Epub 2010/10/16. doi: 10.1161/ATVBAHA.110.210906 20947826
24. Berglund ED, Li CY, Poffenberger G, Ayala JE, Fueger PT, Willis SE, et al. Glucose metabolism in vivo in four commonly used inbred mouse strains. Diabetes. 2008;57(7):1790–9. doi: 10.2337/db07-1615 18398139
25. Taleb S, Herbin O, Ait-Oufella H, Verreth W, Gourdy P, Barateau V, et al. Defective leptin/leptin receptor signaling improves regulatory T cell immune response and protects mice from atherosclerosis. Arterioscler Thromb Vasc Biol. 2007;27(12):2691–8. 17690315
26. Semenkovich CF, Coleman T, Daugherty A, Effects of heterozygous lipoprotein lipase deficiency on diet-induced atherosclerosis in mice. J Lipid Res. 1998;39(6):1141–51. 9643345
27. Storey JD, Tibshirani R, Statistical significance for genomewide studies. Proc Natl Acad Sci U S A. 2003;100(16):9440–5. 12883005
28. Su Z, Ishimori N, Chen Y, Leiter EH, Churchill GA, Paigen B, et al. Four additional mouse crosses improve the lipid QTL landscape and identify Lipg as a QTL gene. J Lipid Res. 2009;50(10):2083–94. doi: 10.1194/jlr.M900076-JLR200 19436067
29. Wergedal JE, Ackert-Bicknell CL, Beamer WG, Mohan S, Baylink DJ, Srivastava AK, Mapping genetic loci that regulate lipid levels in a NZB/B1NJxRF/J intercross and a combined intercross involving NZB/B1NJ, RF/J, MRL/MpJ, and SJL/J mouse strains. J Lipid Res. 2007;48(8):1724–34. 17496333
30. Daugherty A, Mouse models of atherosclerosis. Am J Med Sci. 2002;323(1):3–10. Epub 2002/01/30. 11814139
31. Hsu J, Smith JD, Genetic-genomic replication to identify candidate mouse atherosclerosis modifier genes. J Am Heart Assoc. 2013;2(1):e005421. Epub 2013/03/26. doi: 10.1161/JAHA.112.005421 23525445
32. Wang SS, Schadt EE, Wang H, Wang X, Ingram-Drake L, Shi W, et al. Identification of pathways for atherosclerosis in mice: integration of quantitative trait locus analysis and global gene expression data. Circ Res. 2007;101(3):e11–30. Epub 2007/07/21. 17641228
33. Koltsova EK, Hedrick CC, Ley K, Myeloid cells in atherosclerosis: a delicate balance of anti-inflammatory and proinflammatory mechanisms. Curr Opin Lipidol. 2013;24(5):371–80. doi: 10.1097/MOL.0b013e328363d298 24005215
34. Gjurich BN, Taghavie-Moghadam PL, Ley K, Galkina EV, L-selectin deficiency decreases aortic B1a and Breg subsets and promotes atherosclerosis. Thromb Haemost. 2014;112(4):803–11. doi: 10.1160/TH13-10-0865 24989887
35. Li J, Ley K, Lymphocyte migration into atherosclerotic plaque. Arterioscler Thromb Vasc Biol. 2015;35(1):40–9. doi: 10.1161/ATVBAHA.114.303227 25301842
36. Ley K, Miller YI, Hedrick CC, Monocyte and macrophage dynamics during atherogenesis. Arterioscler Thromb Vasc Biol. 2011;31(7):1506–16. doi: 10.1161/ATVBAHA.110.221127 21677293
37. Zhang X, Goncalves R, Mosser DM, The isolation and characterization of murine macrophages. Curr Protoc Immunol. 2008;Chapter 14:Unit 14 1.
38. Cook AD, Braine EL, Hamilton JA, The phenotype of inflammatory macrophages is stimulus dependent: implications for the nature of the inflammatory response. J Immunol. 2003;171(9):4816–23. 14568960
39. Hussell T, Bell TJ, Alveolar macrophages: plasticity in a tissue-specific context. Nat Rev Immunol. 2014;14(2):81–93. doi: 10.1038/nri3600 24445666
40. Orozco LD, Kapturczak MH, Barajas B, Wang X, Weinstein MM, Wong J, et al. Heme oxygenase-1 expression in macrophages plays a beneficial role in atherosclerosis. Circ Res. 2007;100(12):1703–11. 17495224
41. Orozco LD, Bennett BJ, Farber CR, Ghazalpour A, Pan C, Che N, et al. Unraveling Inflammatory Responses using Systems Genetics and Gene-Environment Interactions in Macrophages. Cell. 2012;151(3):658–70. doi: 10.1016/j.cell.2012.08.043 23101632
42. Shaposhnik Z, Wang X, Weinstein M, Bennett BJ, Lusis AJ, Granulocyte macrophage colony-stimulating factor regulates dendritic cell content of atherosclerotic lesions. Arterioscler Thromb Vasc Biol. 2007;27(3):621–7. Epub 2006/12/13. 17158354
43. Qiao JH, Fishbein MC, Demer LL, Lusis AJ, Genetic determination of cartilaginous metaplasia in mouse aorta. Arterioscler Thromb Vasc Biol. 1995;15(12):2265–72. Epub 1995/12/01. 7489252
44. Bennett BJ, Wang SS, Wang XP, Wu X, Lusis AJ, Genetic Regulation of Atherosclerotic Plaque Size and Morphology in the Innominate Artery of Hyperlipidemic Mice. Arterioscler Thromb Vasc Biol. 2009;29:348–55. Epub 2009/01/06. doi: 10.1161/ATVBAHA.108.176685 19122174
45. Koeth RA, Wang Z, Levison BS, Buffa JA, Org E, Sheehy BT, et al. Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat Med. 2013;19(5):576–85. Epub 2013/04/09. doi: 10.1038/nm.3145 23563705
46. Hecker M, Sessa WC, Harris HJ, Anggard EE, Vane JR, The metabolism of L-arginine and its significance for the biosynthesis of endothelium-derived relaxing factor: cultured endothelial cells recycle L-citrulline to L-arginine. Proc Natl Acad Sci U S A. 1990;87(21):8612–6. 2236071
47. Tong BC, Barbul A, Cellular and physiological effects of arginine. Mini Rev Med Chem. 2004;4(8):823–32. 15544543
48. Romero MJ, Platt DH, Caldwell RB, Caldwell RW, Therapeutic use of citrulline in cardiovascular disease. Cardiovasc Drug Rev. 2006;24(3–4):275–90. 17214603
49. Yang Z, Ming XF, Functions of arginase isoforms in macrophage inflammatory responses: impact on cardiovascular diseases and metabolic disorders. Front Immunol. 2014;5:533. doi: 10.3389/fimmu.2014.00533 25386179
50. Zhou D, Huang C, Lin Z, Zhan S, Kong L, Fang C, et al. Macrophage polarization and function with emphasis on the evolving roles of coordinated regulation of cellular signaling pathways. Cell Signal. 2014;26(2):192–7. doi: 10.1016/j.cellsig.2013.11.004 24219909
51. Dedio J, Konig P, Wohlfart P, Schroeder C, Kummer W, Muller-Esterl W, NOSIP, a novel modulator of endothelial nitric oxide synthase activity. FASEB J. 2001;15(1):79–89. 11149895
52. Langfelder P, Horvath S, WGCNA: an R package for weighted gene co-expression network analysis. BMC Bioinformatics. 2008;9(1):559. Epub 2008/12/31.
53. Teumer A, Holtfreter B, Volker U, Petersmann A, Nauck M, Biffar R, et al. Genome-wide association study of chronic periodontitis in a general German population. J Clin Periodontol. 2013;40(11):977–85. doi: 10.1111/jcpe.12154 24024966
54. Colin E, Huynh Cong E, Mollet G, Guichet A, Gribouval O, Arrondel C, et al. Loss-of-function mutations in WDR73 are responsible for microcephaly and steroid-resistant nephrotic syndrome: Galloway-Mowat syndrome. Am J Hum Genet. 2014;95(6):637–48. doi: 10.1016/j.ajhg.2014.10.011 25466283
55. Lippert C, Listgarten J, Liu Y, Kadie CM, Davidson RI, Heckerman D, FaST linear mixed models for genome-wide association studies. Nat Methods. 2011;8(10):833–5. Epub 2011/09/06. doi: 10.1038/nmeth.1681 21892150
56. Rau CD, Parks B, Wang Y, Eskin E, Simecek P, Churchill GA, et al. High Density Genotypes of Inbred Mouse Strains: Improved Power and Precision of Association Mapping. G3 (Bethesda). 2015.
57. Tenesa A, Haley CS, The heritability of human disease: estimation, uses and abuses. Nat Rev Genet. 2013;14(2):139–49. doi: 10.1038/nrg3377 23329114
58. Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK, Nyholt DR, et al. Common SNPs explain a large proportion of the heritability for human height. Nat Genet. 2010;42(7):565–9. Epub 2010/06/22. doi: 10.1038/ng.608 20562875
59. Kruijer W. Heritability: Marker-Based Estimation of Heritability Using Individual Plant or Plot Data 2015. R package version 1.1: http://CRAN.R-project.org/package=heritability.
60. Consortium CAD, Deloukas P, Kanoni S, Willenborg C, Farrall M, Assimes TL, et al. Large-scale association analysis identifies new risk loci for coronary artery disease. Nat Genet. 2013;45(1):25–33. doi: 10.1038/ng.2480 23202125
61. Lu X, Wang L, Chen S, He L, Yang X, Shi Y, et al. Genome-wide association study in Han Chinese identifies four new susceptibility loci for coronary artery disease. Nat Genet. 2012;44(8):890–4. doi: 10.1038/ng.2337 22751097
62. Erdmann J, Stark K, Esslinger UB, Rumpf PM, Koesling D, de Wit C, et al. Dysfunctional nitric oxide signalling increases risk of myocardial infarction. Nature. 2013;504(7480):432–6. doi: 10.1038/nature12722 24213632
63. Samanta D, Ramagopal UA, Rubinstein R, Vigdorovich V, Nathenson SG, Almo SC, Structure of Nectin-2 reveals determinants of homophilic and heterophilic interactions that control cell-cell adhesion. Proc Natl Acad Sci U S A. 2012;109(37):14836–40. doi: 10.1073/pnas.1212912109 22927415
64. Marchetti G, Girelli D, Zerbinati C, Lunghi B, Friso S, Meneghetti S, et al. An integrated genomic-transcriptomic approach supports a role for the proto-oncogene BCL3 in atherosclerosis. Thromb Haemost. 2014;113(3).
65. Erbilgin A, Siemers N, Kayne P, Yang WP, Berliner J, Lusis AJ, Gene expression analyses of mouse aortic endothelium in response to atherogenic stimuli. Arterioscler Thromb Vasc Biol. 2013;33(11):2509–17. doi: 10.1161/ATVBAHA.113.301989 23990205
66. Venables WN, Ripley B, Linear Statistical Models. Modern Applied Statistics with S. 4th ed: Springer, New York; 2002. p. 139–82.
67. Bennett BJ, de Aguiar Vallim TQ, Wang Z, Shih DM, Meng Y, Gregory J, et al. Trimethylamine-N-oxide, a metabolite associated with atherosclerosis, exhibits complex genetic and dietary regulation. Cell Metab. 2013;17(1):49–60. Epub 2013/01/15. doi: 10.1016/j.cmet.2012.12.011 23312283
68. Moncada S, Palmer RM, Higgs EA, Biosynthesis of nitric oxide from L-arginine. A pathway for the regulation of cell function and communication. Biochemical pharmacology. 1989;38(11):1709–15. 2567594
69. Voight BF, Peloso GM, Orho-Melander M, Frikke-Schmidt R, Barbalic M, Jensen MK, et al. Plasma HDL cholesterol and risk of myocardial infarction: a mendelian randomisation study. Lancet. 2012;380(9841):572–80. doi: 10.1016/S0140-6736(12)60312-2 22607825
70. Hartiala J, Bennett BJ, Tang WH, Wang Z, Stewart AF, Roberts R, et al. Comparative genome-wide association studies in mice and humans for trimethylamine N-oxide, a proatherogenic metabolite of choline and L-carnitine. Arterioscler Thromb Vasc Biol. 2014;34(6):1307–13. Epub 2014/03/29. doi: 10.1161/ATVBAHA.114.303252 24675659
71. Zuk O, Hechter E, Sunyaev SR, Lander ES, The mystery of missing heritability: Genetic interactions create phantom heritability. Proc Natl Acad Sci U S A. 2012;109(4):1193–8. doi: 10.1073/pnas.1119675109 22223662
72. Bloom JS, Ehrenreich IM, Loo WT, Lite TL, Kruglyak L, Finding the sources of missing heritability in a yeast cross. Nature. 2013;494(7436):234–7. doi: 10.1038/nature11867 23376951
73. Peden JF, Farrall M, Thirty-five common variants for coronary artery disease: the fruits of much collaborative labour. Hum Mol Genet. 2011;20(R2):R198–205. doi: 10.1093/hmg/ddr384 21875899
74. Wang SS, Shi W, Wang X, Velky L, Greenlee S, Wang MT, et al. Mapping, genetic isolation, and characterization of genetic loci that determine resistance to atherosclerosis in C3H mice. Arterioscler Thromb Vasc Biol. 2007;27(12):2671–6. 17916774
75. Kayashima Y, Tomita H, Zhilicheva S, Kim S, Kim HS, Bennett BJ, et al. Quantitative trait loci affecting atherosclerosis at the aortic root identified in an intercross between DBA2J and 129S6 apolipoprotein E-null mice. PLoS One. 2014;9(2):e88274. doi: 10.1371/journal.pone.0088274 24586312
76. Su Z, Li Y, James JC, McDuffie M, Matsumoto AH, Helm GA, et al. Quantitative trait locus analysis of atherosclerosis in an intercross between C57BL/6 and C3H mice carrying the mutant apolipoprotein E gene. Genetics. 2006;172(3):1799–807. 16387874
77. Wang Z, Tang WH, Cho L, Brennan DM, Hazen SL, Targeted metabolomic evaluation of arginine methylation and cardiovascular risks: potential mechanisms beyond nitric oxide synthase inhibition. Arterioscler Thromb Vasc Biol. 2009;29(9):1383–91. doi: 10.1161/ATVBAHA.109.185645 19542023
78. Tang WH, Wang Z, Cho L, Brennan DM, Hazen SL, Diminished global arginine bioavailability and increased arginine catabolism as metabolic profile of increased cardiovascular risk. J Am Coll Cardiol. 2009;53(22):2061–7. doi: 10.1016/j.jacc.2009.02.036 19477356
79. Sourij H, Meinitzer A, Pilz S, Grammer TB, Winkelmann BR, Boehm BO, et al. Arginine bioavailability ratios are associated with cardiovascular mortality in patients referred to coronary angiography. Atherosclerosis. 2011;218(1):220–5. doi: 10.1016/j.atherosclerosis.2011.04.041 21632053
80. Koeberl DD, Young SP, Gregersen NS, Vockley J, Smith WE, Benjamin DK, Jr.et al. Rare disorders of metabolism with elevated butyryl- and isobutyryl-carnitine detected by tandem mass spectrometry newborn screening. Pediatr Res. 2003;54(2):219–23. 12736383
81. Schrijvers DM, De Meyer GR, Herman AG, Martinet W, Phagocytosis in atherosclerosis: Molecular mechanisms and implications for plaque progression and stability. Cardiovasc Res. 2007;73(3):470–80. 17084825
82. Babaev VR, Gleaves LA, Carter KJ, Suzuki H, Kodama T, Fazio S, et al. Reduced atherosclerotic lesions in mice deficient for total or macrophage-specific expression of scavenger receptor-A. Arterioscler Thromb Vasc Biol. 2000;20(12):2593–9. 11116058
83. Febbraio M, Podrez EA, Smith JD, Hajjar DP, Hazen SL, Hoff HF, et al. Targeted disruption of the class B scavenger receptor CD36 protects against atherosclerotic lesion development in mice. J Clin Invest. 2000;105(8):1049–56. 10772649
84. Moore KJ, Kunjathoor VV, Koehn SL, Manning JJ, Tseng AA, Silver JM, et al. Loss of receptor-mediated lipid uptake via scavenger receptor A or CD36 pathways does not ameliorate atherosclerosis in hyperlipidemic mice. J Clin Invest. 2005;115(8):2192–201. 16075060
85. Berisha SZ, Hsu J, Robinet P, Smith JD, Transcriptome analysis of genes regulated by cholesterol loading in two strains of mouse macrophages associates lysosome pathway and ER stress response with atherosclerosis susceptibility. PLoS One. 2013;8(5):e65003. doi: 10.1371/journal.pone.0065003 23705026
86. Ross R, Atherosclerosis—an inflammatory disease. N Engl J Med. 1999;340(2):115–26. 9887164
87. Raines EW, Ferri N, Thematic review series: The immune system and atherogenesis. Cytokines affecting endothelial and smooth muscle cells in vascular disease. J Lipid Res. 2005;46(6):1081–92. Epub 2005/04/19. 15834121
88. Inoue T, Komoda H, Nonaka M, Kameda M, Uchida T, Node K, Interleukin-8 as an independent predictor of long-term clinical outcome in patients with coronary artery disease. Int J Cardiol. 2008;124(3):319–25. 17442429
89. Boekholdt SM, Peters RJ, Hack CE, Day NE, Luben R, Bingham SA, et al. IL-8 plasma concentrations and the risk of future coronary artery disease in apparently healthy men and women: the EPIC-Norfolk prospective population study. Arterioscler Thromb Vasc Biol. 2004;24(8):1503–8. 15178568
90. Boisvert WA, Rose DM, Johnson KA, Fuentes ME, Lira SA, Curtiss LK, et al. Up-regulated expression of the CXCR2 ligand KC/GRO-alpha in atherosclerotic lesions plays a central role in macrophage accumulation and lesion progression. Am J Pathol. 2006;168(4):1385–95. 16565511
91. Gerszten RE, Garcia-Zepeda EA, Lim YC, Yoshida M, Ding HA, Gimbrone MA, Jr.et al. MCP-1 and IL-8 trigger firm adhesion of monocytes to vascular endothelium under flow conditions. Nature. 1999;398(6729):718–23. 10227295
92. Karakurum M, Shreeniwas R, Chen J, Pinsky D, Yan SD, Anderson M, et al. Hypoxic induction of interleukin-8 gene expression in human endothelial cells. J Clin Invest. 1994;93(4):1564–70. 8163658
93. Mehrabian M, Qiao JH, Hyman R, Ruddle D, Laughton C, Lusis AJ, Influence of the apoA-II gene locus on HDL levels and fatty streak development in mice. Arterioscler Thromb. 1993;13(1):1–10. 8422330
94. Dutta P, Courties G, Wei Y, Leuschner F, Gorbatov R, Robbins CS, et al. Myocardial infarction accelerates atherosclerosis. Nature. 2012;487(7407):325–9. doi: 10.1038/nature11260 22763456
95. Davis RC, van Nas A, Bennett B, Orozco L, Pan C, Rau CD, et al. Genome-wide association mapping of blood cell traits in mice. Mamm Genome. 2013;24(3–4):105–18. Epub 2013/02/19. doi: 10.1007/s00335-013-9448-0 23417284
96. Kim JB, Deluna A, Mungrue IN, Vu C, Pouldar D, Civelek M, et al. Effect of 9p21.3 coronary artery disease locus neighboring genes on atherosclerosis in mice. Circulation. 2012;126(15):1896–906. doi: 10.1161/CIRCULATIONAHA.111.064881 22952318
97. van den Maagdenberg AM, Hofker MH, Krimpenfort PJ, de Bruijn I, van Vlijmen B, van der Boom H, et al. Transgenic mice carrying the apolipoprotein E3-Leiden gene exhibit hyperlipoproteinemia. J Biol Chem. 1993;268(14):10540–5. Epub 1993/05/15. 7683682
98. Puppione DL, Charugundla S, A microprecipitation technique suitable for measuring alpha-lipoprotein cholesterol. Lipids. 1994;29(8):595–7. Epub 1994/08/01. 7990668
99. Hedrick CC, Castellani LW, Warden CH, Puppione DL, Lusis AJ, Influence of mouse apolipoprotein A-II on plasma lipoproteins in transgenic mice. J Biol Chem. 1993;268(27):20676–82. Epub 1993/09/25. 8376417
100. Shih DM, Xia YR, Wang XP, Miller E, Castellani LW, Subbanagounder G, et al. Combined serum paraoxonase knockout/apolipoprotein E knockout mice exhibit increased lipoprotein oxidation and atherosclerosis. J Biol Chem. 2000;275(23):17527–35. Epub 2000/04/05. 10748217
101. Yeo I-K, Johnson RA, A new family of power transformations to improve normality or symmetry. Biometrika. 2000;87:954–9.
102. Wang Z, Levison BS, Hazen JE, Donahue L, Li XM, Hazen SL, Measurement of trimethylamine-N-oxide by stable isotope dilution liquid chromatography tandem mass spectrometry. Anal Biochem. 2014;455:35–40. doi: 10.1016/j.ab.2014.03.016 24704102
103. Taicher GZ, Tinsley FC, Reiderman A, Heiman ML, Quantitative magnetic resonance (QMR) method for bone and whole-body-composition analysis. Anal Bioanal Chem. 2003;377(6):990–1002. Epub 2003/09/19. 13680051
104. Ghazalpour A, Bennett B, Petyuk VA, Orozco L, Hagopian R, Mungrue IN, et al. Comparative analysis of proteome and transcriptome variation in mouse. PLoS Genet. 2011;7(6):e1001393. Epub 2011/06/23. doi: 10.1371/journal.pgen.1001393 21695224
105. Guo Y, Sheng Q, Li J, Ye F, Samuels DC, Shyr Y, Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data. PLoS One. 2013;8(8):e71462. doi: 10.1371/journal.pone.0071462 23977046
106. Plaisier CL, Horvath S, Huertas-Vazquez A, Cruz-Bautista I, Herrera MF, Tusie-Luna T, et al. A systems genetics approach implicates USF1, FADS3, and other causal candidate genes for familial combined hyperlipidemia. PLoS genetics. 2009;5(9):e1000642. Epub 2009/09/15. doi: 10.1371/journal.pgen.1000642 19750004
107. Gargalovic PS, Imura M, Zhang B, Gharavi NM, Clark MJ, Pagnon J, et al. Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxidized lipids. Proc Natl Acad Sci U S A. 2006;103(34):12741–6. 16912112
108. Oldham MC, Horvath S, Geschwind DH, Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proc Natl Acad Sci U S A. 2006;103(47):17973–8. Epub 2006/11/15. 17101986
109. van Nas A, Guhathakurta D, Wang SS, Yehya N, Horvath S, Zhang B, et al. Elucidating the role of gonadal hormones in sexually dimorphic gene coexpression networks. Endocrinology. 2009;150(3):1235–49. Epub 2008/11/01. doi: 10.1210/en.2008-0563 18974276
110. Park CC, Gale GD, de Jong S, Ghazalpour A, Bennett BJ, Farber CR, et al. Gene networks associated with conditional fear in mice identified using a systems genetics approach. BMC systems biology. 2011;5:43. Epub 2011/03/18. doi: 10.1186/1752-0509-5-43 21410935
111. Zhang B, Horvath S, A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol. 2005;4:Article17. Epub 2006/05/02.
112. Langfelder P, Zhang B, Horvath S, Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics. 2008;24(5):719–20. 18024473
113. Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, et al. A travel guide to Cytoscape plugins. Nature methods. 2012;9(11):1069–76. Epub 2012/11/08. doi: 10.1038/nmeth.2212 23132118
114. Huang da W, Sherman BT, Tan Q, Kir J, Liu D, Bryant D, et al. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 2007;35(Web Server issue):W169–75. Epub 2007/06/20. 17576678
115. Yang H, Ding Y, Hutchins LN, Szatkiewicz J, Bell TA, Paigen BJ, et al. A customized and versatile high-density genotyping array for the mouse. Nat Methods. 2009;6(9):663–6. Epub 2009/08/12. doi: 10.1038/nmeth.1359 19668205
116. Langfelder P, Horvath S, WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9:559. Epub 2008/12/31. doi: 10.1186/1471-2105-9-559 19114008
117. Ghazalpour A, Doss S, Kang H, Farber C, Wen PZ, Brozell A, et al. High-resolution mapping of gene expression using association in an outbred mouse stock. PLoS Genet. 2008;4(8):e1000149. Epub 2008/08/09. doi: 10.1371/journal.pgen.1000149 18688273
118. Pruim RJ, Welch RP, Sanna S, Teslovich TM, Chines PS, Gliedt TP, et al. LocusZoom: regional visualization of genome-wide association scan results. Bioinformatics. 2010;26(18):2336–7. Epub 2010/07/17. doi: 10.1093/bioinformatics/btq419 20634204