Table S6 Found at: doi:10.1371/journal.pone.0001435.s006 (0.08 MB XLS) Table S7 Found at: doi:10.1371/journal.pone.0001435.s007 (1.72 MB XLS) Table S8 Found at: doi:10.1371/journal.pone.0001435.s008 (0.03 MB XLS) Table S9 Found at: doi:10.1371/journal.pone.0001435.s009 (1.42 MB XLS) REFERENCES 1. Brem RB, Yvert G, Clinton R, Kruglyak L (2002) Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752–755. 2. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, et al. (2003) Genetics of gene expression surveyed in maize, mouse and man. Nature 422: 297–302. 3. Cheung VG, Conlin LK, Weber TM, Arcaro M, Jen KY, et al. (2003) Natural variation in human gene expression assessed in lymphoblastoid cells. Nat Genet 33: 422–425. 4. Morley M, Molony CM, Weber TM, Devlin JL, Ewens KG, et al. (2004) Genetic analysis of genome-wide variation in human gene expression. Nature 430: 743–747. 5. Bystrykh L, Weersing E, Dontje B, Sutton S, Pletcher MT, et al. (2005) Uncovering regulatory pathways that affect hematopoietic stem cell function using ‘genetical genomics’. Nat Genet 37: 225–232. 6. Drake TA, Schadt EE, Davis RC, Lusis AJ (2005) Integrating genetic and gene expression data to study the metabolic syndrome and diabetes in mice. Am J Ther 12: 503–511. 7. Drake TA, Schadt EE, Lusis AJ (2006) Integrating genetic and gene expression data: application to cardiovascular and metabolic traits in mice. Mamm Genome 17: 466–479. 8. Ghazalpour A, Doss S, Sheth SS, Ingram-Drake LA, Schadt EE, et al. (2005) Genomic analysis of metabolic pathway gene expression in mice. Genome Biol 6: R59. 9. Ghazalpour A, Doss S, Zhang B, Wang S, Plaisier C, et al. (2006) Integrating genetic and network analysis to characterize genes related to mouse weight. PLoS Genet 2: e130. 10. Meng H, Vera I, Che N, Wang X, Wang SS, et al. (2007) Identification of Abcc6 as the major causal gene for dystrophic cardiac calcification in mice through integrative genomics. Proc Natl Acad Sci U S A 104: 4530–4535. 11. Li AC, Brown KK, Silvestre MJ, Willson TM, Palinski W, et al. (2000) Peroxisome proliferator-activated receptor gamma ligands inhibit development of atherosclerosis in LDL receptor-deficient mice. J Clin Invest 106: 523–531. 12. Wang S, Yehya N, Schadt EE, Wang H, Drake TA, et al. (2006) Genetic and genomic analysis of a fat mass trait with complex inheritance reveals marked sex specificity. PLoS Genet 2: e15. 13. Yang X, Schadt EE, Wang S, Wang H, Arnold AP, et al. (2006) Tissue-specific expression and regulation of sexually dimorphic genes in mice. Genome Res 16: 995–1004. 14. Dansky HM, Shu P, Donavan M, Montagno J, Nagle DL, et al. (2002) A phenotype-sensitizing Apoe-deficient genetic background reveals novel athero- sclerosis predisposition loci in the mouse. Genetics 160: 1599–2608. 15. Smith JD, Bhasin JM, Baglione J, Settle M, Xu Y, et al. (2006) Atherosclerosis susceptibility loci identified from a strain intercross of apolipoprotein E-deficient mice via a high-density genome scan. Arterioscler Thromb Vasc Biol 26: 597–603. 16. Lander E, Kruglyak L (1995) Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nat Genet 11: 241–247. 17. Ng K, Pullirsch D, Leeb M, Wutz A (2007) Xist and the order of silencing. EMBO Rep 8: 34–39. 18. Kobayashi S, Isotani A, Mise N, Yamamoto M, Fujihara Y, et al. (2006) Comparison of gene expression in male and female mouse blastocysts revealed imprinting of the X-linked gene, Rhox5/Pem, at preimplantation stages. Curr Biol 16: 166–172. 19. Chesler EJ, Lu L, Shou S, Qu Y, Gu J, et al. (2005) Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nat Genet 37: 233–242. Sex Specific Gene Regulation Table S10 Found at: doi:10.1371/journal.pone.0001435.s010 (0.08 MB XLS) Author Contributions Conceived and designed the experiments: JS. Performed the experiments: EC DP. Analyzed the data: JS JB AK XC. Contributed reagents/ materials/analysis tools: JB. Wrote the paper: JS JB. 20. Chesler EJ, Bystrykh L, de Hann G, Cooke MP, Su A, et al. (2006) Normalization procedures and detection of linkage signal in genetical-genomics experiments. Nat Genet 38: 856–858. 21. Petretto E, Mangion M, Cook SA, Aitman TJ, Pravenec M, et al. (2006) Normalization procedures and detection of linkage signal in genetical-genomics experiments. Nat Genet 38: 858–859. 22. Yvert G, Brem RB, Whittle J, Akey JM, Foss E, et al. (2003) Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat Genet 35: 57–64. 23. Akiyama H, Fujisawa N, Tashiro Y, Takanabe N, Sugiyama A, et al. (2003) The role of transcriptional corepressor Nif3l1 in early stage of neural differentiation via cooperation with Trip15/CSN2. J Biol Chem 278: 10752–10762. 24. Merla G, Howald C, Antonarakis SE, Reymond A (2004) The subcellular localization of the ChoRE-binding protein, encoded by the Williams-Beuren syndrome critical region gene 14, is regulated by 14-3-3. Hum Mol Genet 13: 1505–1514. 25. Dai Z, Pendergast AM (1995) Abi-2, a novel SH3-containing protein interacts with the c-Abl tyrosine kinase and modulates c-Abl transforming activity. Genes Dev 9: 2569–2582. 26. Grove M, Demyanenko G, Echarri A, Zipfel PA, Quiroz ME, et al. (2004) ABI2- deficient mice exhibit defective cell migration, aberrant dendritic spine morphogenesis, and deficits in learning and memory. Mol Cell Biol 24: 10905–10922. 27. Charng MJ, Zhang D, Kinnunen P, Schneider MD (1998) A novel protein distinguishes between quiescent and activated forms of the type I transforming growth factor beta receptor. J Biol Chem 273: 9365–9368. 28. Wurthner JU, Frank DB, Felici A, Green HM, Cao Z, et al. (2001) Transforming growth factor-beta receptor-associated protein 1 is a Smad4 chaperone. J Biol Chem 276: 19495–19502. 29. Fitzgerald J, Kennedy D, Viseshakul N, Cohen BN, Mattick J, et al. (2000) UNCL, the mammalian homologue of UNC-50, is an inner nuclear membrane RNA-binding protein. Brain Res 877: 110–123. 30. Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, et al. (2004) The Microprocessor complex mediates the genesis of microRNAs. Nature 432: 235–240. 31. Yeom KH, Lee Y, Han J, Suh MR, Kim VN (2006) Characterization of DGCR8/Pasha, the essential cofactor for Drosha in primary miRNA processing. Nucleic Acids Res 34: 4622–4629. 32. Wang Y, Medvid R, Melton C, Jaenisch R, Blelloch R (2007) DGCR8 is essential for microRNA biogenesis and silencing of embryonic stem cell self- renewal. Nat Genet 39: 380–385. 33. Peirce JL, Li H, Wang J, Manly KF, Hitzemann RJ, et al. (2006) How replicable are mRNA expression QTL? Mamm Genome 17: 643–656. 34. Plump AS, Smith JD, Hayek T, Aalto-Setala K, Walsh A, et al. (1992) Severe hypercholesterolemia and atherosclerosis in apolipoprotein E-deficient mice created by homologous recombination in ES cells. Cell 71: 343–353. 35. Smith JD, Peng DQ, Dansky HM, Settle M, Baglione J, et al. (2006) Transcriptome profile of macrophages from atherosclerosis-sensitive and atherosclerosis-resistant mice. Mamm Genome 17: 220–229. 36. Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19: 889–890. 37. Beissbarth T, Speed TP (2004) GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 20: 1464–1465. PLoS ONE | www.plosone.org 8 January 2008 | Issue 1 | e1435