메뉴 건너뛰기




Volumn 26, Issue 6, 2016, Pages 768-777

Impact of the X chromosome and sex on regulatory variation

(19)  Kukurba, Kimberly R a   Parsana, Princy b   Balliu, Brunilda a   Smith, Kevin S a   Zappala, Zachary a   Knowles, David A b   Favé, Marie Julie c   Davis, Joe R a   Li, Xin a   Zhu, Xiaowei a   Potash, James B d   Weissman, Myrna M e   Shi, Jianxin f   Kundaje, Anshul a,g   Levinson, Douglas F a   Awadalla, Philip c   Mostafavi, Sara h   Battle, Alexis b   Montgomery, Stephen B a,g  


Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

EID: 84973309378     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.197897.115     Document Type: Article
Times cited : (75)

References (74)
  • 1
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biol 11: R106.
    • (2010) Genome Biol , vol.11 , pp. R106
    • Anders, S.1    Huber, W.2
  • 2
    • 0035107550 scopus 로고    scopus 로고
    • Contrasting patterns of X-linked and autosomal nucleotide variation in drosophila melanogaster and drosophila simulans
    • Andolfatto P. 2001. Contrasting patterns of X-linked and autosomal nucleotide variation in Drosophila melanogaster and Drosophila simulans. Mol Biol Evol 18: 279-290.
    • (2001) Mol Biol Evol , vol.18 , pp. 279-290
    • Andolfatto, P.1
  • 3
    • 84878835954 scopus 로고    scopus 로고
    • Cohort profile of the CARTaGENE study: Quebec's population-based biobank for public health and personalized genomics
    • Awadalla P, Boileau C, Payette Y, Idaghdour Y, Goulet JP, Knoppers B, Hamet P, Laberge C; CARTaGENE Project. 2013. Cohort profile of the CARTaGENE study: Quebec's population-based biobank for public health and personalized genomics. Int J Epidemiol 42: 1285-1299.
    • (2013) Int J Epidemiol , vol.42 , pp. 1285-1299
    • Awadalla, P.1    Boileau, C.2    Payette, Y.3    Idaghdour, Y.4    Goulet, J.P.5    Knoppers, B.6    Hamet, P.7    Laberge, C.8
  • 5
    • 84973315903 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B Methodol 57: 289-300.
    • (1995) J R Stat Soc B Methodol , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 7
    • 1842453957 scopus 로고    scopus 로고
    • Subgroup analyses in randomized trials: Risks of subgroup-specific analyses; power and sample size for the interaction test
    • Brookes ST, Whitely E, Egger M, Smith GD, Mulheran PA, Peters TJ. 2004. Subgroup analyses in randomized trials: risks of subgroup-specific analyses; power and sample size for the interaction test. J Clin Epidemiol 57: 229-236.
    • (2004) J Clin Epidemiol , vol.57 , pp. 229-236
    • Brookes, S.T.1    Whitely, E.2    Egger, M.3    Smith, G.D.4    Mulheran, P.A.5    Peters, T.J.6
  • 8
    • 84888877924 scopus 로고    scopus 로고
    • Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
    • Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. 2013. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10: 1213-1218.
    • (2013) Nat Methods , vol.10 , pp. 1213-1218
    • Buenrostro, J.D.1    Giresi, P.G.2    Zaba, L.C.3    Chang, H.Y.4    Greenleaf, W.J.5
  • 9
    • 15244353967 scopus 로고    scopus 로고
    • X-inactivation profile reveals extensive variability in X-linked gene expression in females
    • Carrel L, Willard HF. 2005. X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature 434: 400-404.
    • (2005) Nature , vol.434 , pp. 400-404
    • Carrel, L.1    Willard, H.F.2
  • 12
    • 84865170739 scopus 로고    scopus 로고
    • Hormonal and chemical regulation of paraoxonases in mice
    • Cheng X, Klaassen CD. 2012. Hormonal and chemical regulation of paraoxonases in mice. J Pharmacol Exp Ther 342: 688-695.
    • (2012) J Pharmacol Exp Ther , vol.342 , pp. 688-695
    • Cheng, X.1    Klaassen, C.D.2
  • 18
    • 4444258534 scopus 로고    scopus 로고
    • Chromatin architecture of the human genome: Gene-rich domains are enriched in open chromatin fibers
    • Gilbert N, Boyle S, Fiegler H, Woodfine K, Carter NP, Bickmore WA. 2004. Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers. Cell 118: 555-566.
    • (2004) Cell , vol.118 , pp. 555-566
    • Gilbert, N.1    Boyle, S.2    Fiegler, H.3    Woodfine, K.4    Carter, N.P.5    Bickmore, W.A.6
  • 19
    • 84875969029 scopus 로고    scopus 로고
    • Gender differences in brain susceptibility to oxidative stress are mediatedby levels ofparaoxonase-2 expression
    • Giordano G, Tait L, Furlong CE, Cole TB, Kavanagh TJ, Costa LG. 2013. Gender differences in brain susceptibility to oxidative stress are mediatedby levels ofparaoxonase-2 expression. Free Radic Biol Med 58: 98-108.
    • (2013) Free Radic Biol Med , vol.58 , pp. 98-108
    • Giordano, G.1    Tait, L.2    Furlong, C.E.3    Cole, T.B.4    Kavanagh, T.J.5    Costa, L.G.6
  • 20
    • 79960899810 scopus 로고    scopus 로고
    • Analyses of X linked and autosomal genetic variation in population-scale whole genome sequencing
    • Gottipati S, Arbiza L, Siepel A, Clark AG, Keinan A. 2011. Analyses of X linked and autosomal genetic variation in population-scale whole genome sequencing. Nat Genet 43: 741-743.
    • (2011) Nat Genet , vol.43 , pp. 741-743
    • Gottipati, S.1    Arbiza, L.2    Siepel, A.3    Clark, A.G.4    Keinan, A.5
  • 21
    • 84929001104 scopus 로고    scopus 로고
    • The genotype-tissue expression (GTEx) pilot analysis: Multitissue gene regulation in humans
    • The GTEx Consortium. 2015. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science 348: 648-660.
    • (2015) Science , vol.348 , pp. 648-660
  • 23
    • 85047686025 scopus 로고    scopus 로고
    • Development of gender differences in depression: An elaborated cognitive vulnerability-transactional stress theory
    • Hankin BL, Abramson LY. 2001. Development of gender differences in depression: an elaborated cognitive vulnerability-transactional stress theory. Psychol Bull 127: 773-796.
    • (2001) Psychol Bull , vol.127 , pp. 773-796
    • Hankin, B.L.1    Abramson, L.Y.2
  • 26
    • 84894260698 scopus 로고    scopus 로고
    • Exploiting gene expression variation to capture gene-environment interactions for disease
    • Idaghdour Y, Awadalla P. 2012. Exploiting gene expression variation to capture gene-environment interactions for disease. Front Genet 3: 228.
    • (2012) Front Genet , vol.3 , pp. 228
    • Idaghdour, Y.1    Awadalla, P.2
  • 27
    • 84882678911 scopus 로고    scopus 로고
    • Differential regulation of cell death programs in males and females by poly (ADP-ribose) polymerase-1 and 17β estradiol
    • Jog NR, Caricchio R. 2013. Differential regulation of cell death programs in males and females by Poly (ADP-Ribose) Polymerase-1 and 17β estradiol. Cell Death Dis 4: e758.
    • (2013) Cell Death Dis , vol.4 , pp. e758
    • Jog, N.R.1    Caricchio, R.2
  • 28
    • 58149151065 scopus 로고    scopus 로고
    • Accelerated genetic drift on chromosome X during the human dispersal out of Africa
    • Keinan A, Mullikin JC, Patterson N, Reich D. 2009. Accelerated genetic drift on chromosome X during the human dispersal out of Africa. Nat Genet 41: 66-70.
    • (2009) Nat Genet , vol.41 , pp. 66-70
    • Keinan, A.1    Mullikin, J.C.2    Patterson, N.3    Reich, D.4
  • 29
    • 82255179690 scopus 로고    scopus 로고
    • Evidence for dosage compensation between the X chromosome and autosomes in mammals
    • Kharchenko PV, Xi R, Park PJ. 2011. Evidence for dosage compensation between the X chromosome and autosomes in mammals. Nat Genet 43: 1167-1169.
    • (2011) Nat Genet , vol.43 , pp. 1167-1169
    • Kharchenko, P.V.1    Xi, R.2    Park, P.J.3
  • 31
    • 47749128919 scopus 로고    scopus 로고
    • Pathways to ischemic neuronal cell death: Are sex differences relevant?
    • Lang JT, McCullough LD. 2008. Pathways to ischemic neuronal cell death: Are sex differences relevant? J Transl Med 6: 33.
    • (2008) J Transl Med , vol.6 , pp. 33
    • Lang, J.T.1    McCullough, L.D.2
  • 33
    • 0022656719 scopus 로고
    • Patterns of coronary heart disease morbidity and mortality in the sexes: A 26-year follow-up of the framingham population
    • Lerner DJ, Kannel WB. 1986. Patterns of coronary heart disease morbidity and mortality in the sexes: a 26-year follow-up of the Framingham population. Am Heart J 111: 383-390.
    • (1986) Am Heart J , vol.111 , pp. 383-390
    • Lerner, D.J.1    Kannel, W.B.2
  • 36
    • 84859504942 scopus 로고    scopus 로고
    • Sex differences in disease risk from reported genome-wide association study findings
    • Liu LY, Schaub MA, Sirota M, Butte AJ. 2012b. Sex differences in disease risk from reported genome-wide association study findings. Hum Genet 131: 353-364.
    • (2012) Hum Genet , vol.131 , pp. 353-364
    • Liu, L.Y.1    Schaub, M.A.2    Sirota, M.3    Butte, A.J.4
  • 37
    • 15244356879 scopus 로고    scopus 로고
    • Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee
    • Lu J, Wu CI. 2005. Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee. Proc Natl Acad Sci 102: 4063-4067.
    • (2005) Proc Natl Acad Sci , vol.102 , pp. 4063-4067
    • Lu, J.1    Wu, C.I.2
  • 38
    • 0035172743 scopus 로고    scopus 로고
    • Sample size determination for studies of gene-environment interaction
    • Luan JA, Wong MY, Day NE, Wareham NJ. 2001. Sample size determination for studies of gene-environment interaction. Int J Epidemiol 30: 1035-1040.
    • (2001) Int J Epidemiol , vol.30 , pp. 1035-1040
    • Luan, J.A.1    Wong, M.Y.2    Day, N.E.3    Wareham, N.J.4
  • 39
    • 20444398494 scopus 로고    scopus 로고
    • Molecular and cellular basis of cardiovascular gender differences
    • Mendelsohn ME, Karas RH. 2005. Molecular and cellular basis of cardiovascular gender differences. Science 308: 1583-1587.
    • (2005) Science , vol.308 , pp. 1583-1587
    • Mendelsohn, M.E.1    Karas, R.H.2
  • 45
    • 34447327216 scopus 로고    scopus 로고
    • Gender disparity in liver cancer due to sex differences in MyD88-dependent IL-6 production
    • Naugler WE, Sakurai T, Kim S, Maeda S, Kim K, Elsharkawy AM, Karin M. 2007. Gender disparity in liver cancer due to sex differences in MyD88-dependent IL-6 production. Science 317: 121-124.
    • (2007) Science , vol.317 , pp. 121-124
    • Naugler, W.E.1    Sakurai, T.2    Kim, S.3    Maeda, S.4    Kim, K.5    Elsharkawy, A.M.6    Karin, M.7
  • 47
    • 77951439152 scopus 로고    scopus 로고
    • Trait-associated SNPs are more likely to be eQTLs: Annotation to enhance discovery from GWAS
    • Nicolae DL, Gamazon E, Zhang W, Duan SW, Dolan ME, Cox NJ. 2010. Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet 6: e1000888.
    • (2010) PLoS Genet , vol.6
    • Nicolae, D.L.1    Gamazon, E.2    Zhang, W.3    Duan, S.W.4    Dolan, M.E.5    Cox, N.J.6
  • 48
    • 56549099067 scopus 로고    scopus 로고
    • Sex-specific genetic architecture of human disease
    • Ober C, Loisel DA, Gilad Y. 2008. Sex-specific genetic architecture of human disease. Nat Rev Genet 9: 911-922.
    • (2008) Nat Rev Genet , vol.9 , pp. 911-922
    • Ober, C.1    Loisel, D.A.2    Gilad, Y.3
  • 49
    • 77958117538 scopus 로고    scopus 로고
    • Strong purifying selection at genes escaping X chromosome inactivation
    • Park C, Carrel L, Makova KD. 2010. Strong purifying selection at genes escaping X chromosome inactivation. Mol Biol Evol 27: 2446-2450.
    • (2010) Mol Biol Evol , vol.27 , pp. 2446-2450
    • Park, C.1    Carrel, L.2    Makova, K.D.3
  • 50
    • 34548057801 scopus 로고    scopus 로고
    • Claims of sex differences: An empirical assessment in genetic associations
    • Patsopoulos NA, Tatsioni A, Ioannidis JP. 2007. Claims of sex differences: an empirical assessment in genetic associations. JAMA 298: 880-893.
    • (2007) JAMA , vol.298 , pp. 880-893
    • Patsopoulos, N.A.1    Tatsioni, A.2    Ioannidis, J.P.3
  • 52
    • 0032845825 scopus 로고    scopus 로고
    • Gender differences in the epidemiology and treatment of anxiety disorders
    • Pigott TA 1999. Gender differences in the epidemiology and treatment of anxiety disorders. J Clin Psychiatry 60(Suppl 18): 4-15.
    • (1999) J Clin Psychiatry , vol.60 , pp. 4-15
    • Pigott, T.A.1
  • 53
    • 84901793865 scopus 로고    scopus 로고
    • Antioxidant defense enzyme genes and asthma susceptibility: Gender-specific effects and heterogeneity in gene-gene interactions between pathogenetic variants of the disease
    • Polonikov AV, Ivanov VP, Bogomazov AD, Freidin MB, Illig T, Solodilova MA. 2014. Antioxidant defense enzyme genes and asthma susceptibility: gender-specific effects and heterogeneity in gene-gene interactions between pathogenetic variants of the disease. Biomed Res Int 2014: 708903.
    • (2014) Biomed Res Int , vol.2014
    • Polonikov, A.V.1    Ivanov, V.P.2    Bogomazov, A.D.3    Freidin, M.B.4    Illig, T.5    Solodilova, M.A.6
  • 55
    • 0037504137 scopus 로고    scopus 로고
    • Sex-dependent gene expression and evolution of the drosophila transcriptome
    • Ranz JM, Castillo-Davis CI, Meiklejohn CD, Hartl DL. 2003. Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science 300: 1742-1745.
    • (2003) Science , vol.300 , pp. 1742-1745
    • Ranz, J.M.1    Castillo-Davis, C.I.2    Meiklejohn, C.D.3    Hartl, D.L.4
  • 57
    • 0021554565 scopus 로고
    • Sex chromosomes and the evolution of sexual dimorphism
    • Rice WR 1984. Sex chromosomes and the evolution of sexual dimorphism. Evolution 38: 735-742.
    • (1984) Evolution , vol.38 , pp. 735-742
    • Rice, W.R.1
  • 58
    • 0346728470 scopus 로고    scopus 로고
    • The X chromosome in population genetics
    • Schaffner SF 2004. The X chromosome in population genetics. Nat Rev Genet 5: 43-51.
    • (2004) Nat Rev Genet , vol.5 , pp. 43-51
    • Schaffner, S.F.1
  • 59
    • 36849074774 scopus 로고    scopus 로고
    • Dynamics and interplay of nuclear architecture, genome organization, and gene expression
    • Schneider R, Grosschedl R. 2007. Dynamics and interplay of nuclear architecture, genome organization, and gene expression. Genes Dev 21: 3027-3043.
    • (2007) Genes Dev , vol.21 , pp. 3027-3043
    • Schneider, R.1    Grosschedl, R.2
  • 60
    • 84861153094 scopus 로고    scopus 로고
    • Matrix eQTL: Ultra fast eQTL analysis via large matrix operations
    • Shabalin AA 2012. Matrix eQTL: ultra fast eQTL analysis via large matrix operations. Bioinformatics 28: 1353-1358.
    • (2012) Bioinformatics , vol.28 , pp. 1353-1358
    • Shabalin, A.A.1
  • 61
    • 58149191893 scopus 로고    scopus 로고
    • Evolution of gene function on the X chromosome versus the autosomes
    • Singh ND, Petrov DA. 2007. Evolution of gene function on the X chromosome versus the autosomes. Genome Dyn 3: 101-118.
    • (2007) Genome Dyn , vol.3 , pp. 101-118
    • Singh, N.D.1    Petrov, D.A.2
  • 62
    • 84881662190 scopus 로고    scopus 로고
    • What is the significance of difference in phenotypic variability across SNP enotypes?
    • Sun X, Elston R, Morris N, Zhu X. 2013. What is the significance of difference in phenotypic variability across SNP enotypes? Am J Hum Genet 93: 390-397.
    • (2013) Am J Hum Genet , vol.93 , pp. 390-397
    • Sun, X.1    Elston, R.2    Morris, N.3    Zhu, X.4
  • 64
    • 84888367236 scopus 로고    scopus 로고
    • Widespread sex differences in gene expression and splicing in the adult human brain
    • Trabzuni D, Ramasamy A, Imran S, Walker R, Smith C, Weale ME, Hardy J, Ryten M, North American Brain Expression Consortium. 2013. Widespread sex differences in gene expression and splicing in the adult human brain. Nat Commun 4: 2771.
    • (2013) Nat Commun , vol.4 , pp. 2771
    • Trabzuni, D.1    Ramasamy, A.2    Imran, S.3    Walker, R.4    Smith, C.5    Weale, M.E.6    Hardy, J.7    Ryten, M.8
  • 66
    • 33746218184 scopus 로고    scopus 로고
    • Evolution on the X chromosome: Unusual patterns and processes
    • Vicoso B, Charlesworth B. 2006. Evolution on the X chromosome: unusual patterns and processes. Nat Rev Genet 7: 645-653.
    • (2006) Nat Rev Genet , vol.7 , pp. 645-653
    • Vicoso, B.1    Charlesworth, B.2
  • 67
    • 44949217429 scopus 로고    scopus 로고
    • A computational model for sex-specific genetic architecture of complex traits in humans: Implications for mapping pain sensitivity
    • Wang C, Cheng Y, Liu T, Li Q, Fillingim RB, Wallace MR, Staud R, Kaplan L, Wu R. 2008. A computational model for sex-specific genetic architecture of complex traits in humans: implications for mapping pain sensitivity. Mol Pain 4: 13.
    • (2008) Mol Pain , vol.4 , pp. 13
    • Wang, C.1    Cheng, Y.2    Liu, T.3    Li, Q.4    Fillingim, R.B.5    Wallace, M.R.6    Staud, R.7    Kaplan, L.8    Wu, R.9
  • 69
    • 0035554904 scopus 로고    scopus 로고
    • Sex differences in autoimmune disease
    • Whitacre CC 2001. Sex differences in autoimmune disease. Nat Immunol 2: 777-780.
    • (2001) Nat Immunol , vol.2 , pp. 777-780
    • Whitacre, C.C.1
  • 71
    • 84877306707 scopus 로고    scopus 로고
    • Exclusion: Toward integrating the X chromosome in genome-wide association analyses
    • Wise AL, Gyi L, Manolio TA. 2013. eXclusion: toward integrating the X chromosome in genome-wide association analyses. Am J Hum Genet 92: 643-647.
    • (2013) Am J Hum Genet , vol.92 , pp. 643-647
    • Wise, A.L.1    Gyi, L.2    Manolio, T.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.