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Volumn 10, Issue 7, 2014, Pages

Cis and Trans Effects of Human Genomic Variants on Gene Expression

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CIS GENE; COHORT ANALYSIS; CONTROLLED STUDY; COPY NUMBER VARIATION; FEMALE; GENE; GENE EXPRESSION REGULATION; GENE LINKAGE DISEQUILIBRIUM; GENE REGULATORY NETWORK; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC VARIABILITY; HUMAN; HUMAN CELL; LONGITUDINAL STUDY; LYMPHOBLASTOID CELL LINE; MALE; QUANTITATIVE TRAIT LOCUS; SAMPLE SIZE; SINGLE NUCLEOTIDE POLYMORPHISM; TRANS GENE; GENETICS; GENOMICS; HUMAN GENOME; PHENOTYPE; TUMOR CELL LINE;

EID: 84905484562     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1004461     Document Type: Article
Times cited : (99)

References (41)
  • 1
    • 67249117049 scopus 로고    scopus 로고
    • Potential etiologic and functional implications of genome-wide association loci for human diseases and traits
    • Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A 106: 9362-9367.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 9362-9367
    • Hindorff, L.A.1    Sethupathy, P.2    Junkins, H.A.3    Ramos, E.M.4    Mehta, J.P.5
  • 2
    • 84866871814 scopus 로고    scopus 로고
    • Mapping cis- and trans-regulatory effects across multiple tissues in twins
    • Grundberg E, Small KS, Hedman AK, Nica AC, Buil A, et al. (2012) Mapping cis- and trans-regulatory effects across multiple tissues in twins. Nat Genet 44: 1084-1089.
    • (2012) Nat Genet , vol.44 , pp. 1084-1089
    • Grundberg, E.1    Small, K.S.2    Hedman, A.K.3    Nica, A.C.4    Buil, A.5
  • 3
    • 77952367694 scopus 로고    scopus 로고
    • Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations
    • Nica AC, Montgomery SB, Dimas AS, Stranger BE, Beazley C, et al. (2010) Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. PLoS Genet 6: e1000895.
    • (2010) PLoS Genet , vol.6
    • Nica, A.C.1    Montgomery, S.B.2    Dimas, A.S.3    Stranger, B.E.4    Beazley, C.5
  • 5
    • 69949176863 scopus 로고    scopus 로고
    • Common regulatory variation impacts gene expression in a cell type-dependent manner
    • Dimas AS, Deutsch S, Stranger BE, Montgomery SB, Borel C, et al. (2009) Common regulatory variation impacts gene expression in a cell type-dependent manner. Science 325: 1246-1250.
    • (2009) Science , vol.325 , pp. 1246-1250
    • Dimas, A.S.1    Deutsch, S.2    Stranger, B.E.3    Montgomery, S.B.4    Borel, C.5
  • 6
    • 77950458649 scopus 로고    scopus 로고
    • Transcriptome genetics using second generation sequencing in a Caucasian population
    • Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, et al. (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464: 773-777.
    • (2010) Nature , vol.464 , pp. 773-777
    • Montgomery, S.B.1    Sammeth, M.2    Gutierrez-Arcelus, M.3    Lach, R.P.4    Ingle, C.5
  • 7
    • 77950460661 scopus 로고    scopus 로고
    • Understanding mechanisms underlying human gene expression variation with RNA sequencing
    • Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, et al. (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464: 768-772.
    • (2010) Nature , vol.464 , pp. 768-772
    • Pickrell, J.K.1    Marioni, J.C.2    Pai, A.A.3    Degner, J.F.4    Engelhardt, B.E.5
  • 8
    • 33846978695 scopus 로고    scopus 로고
    • Relative impact of nucleotide and copy number variation on gene expression phenotypes
    • Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, et al. (2007) Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315: 848-853.
    • (2007) Science , vol.315 , pp. 848-853
    • Stranger, B.E.1    Forrest, M.S.2    Dunning, M.3    Ingle, C.E.4    Beazley, C.5
  • 9
    • 79952256739 scopus 로고    scopus 로고
    • The architecture of gene regulatory variation across multiple human tissues: the MuTHER study
    • Nica AC, Parts L, Glass D, Nisbet J, Barrett A, et al. (2011) The architecture of gene regulatory variation across multiple human tissues: the MuTHER study. PLoS Genet 7: e1002003.
    • (2011) PLoS Genet , vol.7
    • Nica, A.C.1    Parts, L.2    Glass, D.3    Nisbet, J.4    Barrett, A.5
  • 10
    • 79959916375 scopus 로고    scopus 로고
    • A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort
    • Greenawalt DM, Dobrin R, Chudin E, Hatoum IJ, Suver C, et al. (2011) A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort. Genome Res 21: 1008-1016.
    • (2011) Genome Res , vol.21 , pp. 1008-1016
    • Greenawalt, D.M.1    Dobrin, R.2    Chudin, E.3    Hatoum, I.J.4    Suver, C.5
  • 11
    • 84878497307 scopus 로고    scopus 로고
    • Global properties and functional complexity of human gene regulatory variation
    • Gaffney DJ, (2013) Global properties and functional complexity of human gene regulatory variation. PLoS Genet 9: e1003501.
    • (2013) PLoS Genet , vol.9
    • Gaffney, D.J.1
  • 12
    • 79952902493 scopus 로고    scopus 로고
    • From expression QTLs to personalized transcriptomics
    • Montgomery SB, Dermitzakis ET, (2011) From expression QTLs to personalized transcriptomics. Nat Rev Genet 12: 277-282.
    • (2011) Nat Rev Genet , vol.12 , pp. 277-282
    • Montgomery, S.B.1    Dermitzakis, E.T.2
  • 13
    • 80053149973 scopus 로고    scopus 로고
    • Allelic heterogeneity and more detailed analyses of known loci explain additional phenotypic variation and reveal complex patterns of association
    • Wood AR, Hernandez DG, Nalls MA, Yaghootkar H, Gibbs JR, et al. (2011) Allelic heterogeneity and more detailed analyses of known loci explain additional phenotypic variation and reveal complex patterns of association. Hum Mol Genet 20: 4082-4092.
    • (2011) Hum Mol Genet , vol.20 , pp. 4082-4092
    • Wood, A.R.1    Hernandez, D.G.2    Nalls, M.A.3    Yaghootkar, H.4    Gibbs, J.R.5
  • 14
    • 84878475112 scopus 로고    scopus 로고
    • Congruence of additive and non-additive effects on gene expression estimated from pedigree and SNP data
    • Powell JE, Henders AK, McRae AF, Kim J, Hemani G, et al. (2013) Congruence of additive and non-additive effects on gene expression estimated from pedigree and SNP data. PLoS Genet 9: e1003502.
    • (2013) PLoS Genet , vol.9
    • Powell, J.E.1    Henders, A.K.2    McRae, A.F.3    Kim, J.4    Hemani, G.5
  • 15
    • 78649783848 scopus 로고    scopus 로고
    • Gene expression in skin and lymphoblastoid cells: Refined statistical method reveals extensive overlap in cis-eQTL signals
    • Ding J, Gudjonsson JE, Liang L, Stuart PE, Li Y, et al. (2010) Gene expression in skin and lymphoblastoid cells: Refined statistical method reveals extensive overlap in cis-eQTL signals. Am J Hum Genet 87: 779-789.
    • (2010) Am J Hum Genet , vol.87 , pp. 779-789
    • Ding, J.1    Gudjonsson, J.E.2    Liang, L.3    Stuart, P.E.4    Li, Y.5
  • 16
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genomewide studies
    • Storey JD, Tibshirani R, (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100: 9440-9445.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2
  • 17
    • 84885645853 scopus 로고    scopus 로고
    • Transcriptome and genome sequencing uncovers functional variation in humans
    • Lappalainen T, Sammeth M, Friedlander MR, Hoen PA, Monlong J, et al. (2013) Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501: 506-511.
    • (2013) Nature , vol.501 , pp. 506-511
    • Lappalainen, T.1    Sammeth, M.2    Friedlander, M.R.3    Hoen, P.A.4    Monlong, J.5
  • 18
    • 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 S, Dolan ME, et al. (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.4    Dolan, M.E.5
  • 19
    • 84885018609 scopus 로고    scopus 로고
    • Systematic identification of trans eQTLs as putative drivers of known disease associations
    • Westra HJ, Peters MJ, Esko T, Yaghootkar H, Schurmann C, et al. (2013) Systematic identification of trans eQTLs as putative drivers of known disease associations. Nat Genet 45: 1238-1243.
    • (2013) Nat Genet , vol.45 , pp. 1238-1243
    • Westra, H.J.1    Peters, M.J.2    Esko, T.3    Yaghootkar, H.4    Schurmann, C.5
  • 20
    • 56449097442 scopus 로고    scopus 로고
    • Batf3 deficiency reveals a critical role for CD8alpha+ dendritic cells in cytotoxic T cell immunity
    • Hildner K, Edelson BT, Purtha WE, Diamond M, Matsushita H, et al. (2008) Batf3 deficiency reveals a critical role for CD8alpha+ dendritic cells in cytotoxic T cell immunity. Science 322: 1097-1100.
    • (2008) Science , vol.322 , pp. 1097-1100
    • Hildner, K.1    Edelson, B.T.2    Purtha, W.E.3    Diamond, M.4    Matsushita, H.5
  • 21
    • 67651001561 scopus 로고    scopus 로고
    • The AP-1 transcription factor Batf controls T(H)17 differentiation
    • Schraml BU, Hildner K, Ise W, Lee WL, Smith WA, et al. (2009) The AP-1 transcription factor Batf controls T(H)17 differentiation. Nature 460: 405-409.
    • (2009) Nature , vol.460 , pp. 405-409
    • Schraml, B.U.1    Hildner, K.2    Ise, W.3    Lee, W.L.4    Smith, W.A.5
  • 22
    • 4544244485 scopus 로고    scopus 로고
    • Hmx2 and Hmx3 homeobox genes direct development of the murine inner ear and hypothalamus and can be functionally replaced by Drosophila Hmx
    • Wang W, Grimmer JF, Van De Water TR, Lufkin T, (2004) Hmx2 and Hmx3 homeobox genes direct development of the murine inner ear and hypothalamus and can be functionally replaced by Drosophila Hmx. Dev Cell 7: 439-453.
    • (2004) Dev Cell , vol.7 , pp. 439-453
    • Wang, W.1    Grimmer, J.F.2    Van De Water, T.R.3    Lufkin, T.4
  • 23
    • 63749090180 scopus 로고    scopus 로고
    • Molecular (SNP) analyses of overlapping hemizygous deletions of 10q25.3 to 10qter in four patients: evidence for HMX2 and HMX3 as candidate genes in hearing and vestibular function
    • Miller ND, Nance MA, Wohler ES, Hoover-Fong JE, Lisi E, et al. (2009) Molecular (SNP) analyses of overlapping hemizygous deletions of 10q25.3 to 10qter in four patients: evidence for HMX2 and HMX3 as candidate genes in hearing and vestibular function. Am J Med Genet A 149A: 669-680.
    • (2009) Am J Med Genet A , vol.149 A , pp. 669-680
    • Miller, N.D.1    Nance, M.A.2    Wohler, E.S.3    Hoover-Fong, J.E.4    Lisi, E.5
  • 24
    • 0042635657 scopus 로고    scopus 로고
    • Expression of the Wdr9 gene and protein products during mouse development
    • Huang H, Rambaldi I, Daniels E, Featherstone M, (2003) Expression of the Wdr9 gene and protein products during mouse development. Dev Dyn 227: 608-614.
    • (2003) Dev Dyn , vol.227 , pp. 608-614
    • Huang, H.1    Rambaldi, I.2    Daniels, E.3    Featherstone, M.4
  • 25
    • 67650258730 scopus 로고    scopus 로고
    • Disentangling molecular relationships with a causal inference test
    • Millstein J, Zhang B, Zhu J, Schadt EE, (2009) Disentangling molecular relationships with a causal inference test. BMC Genet 10: 23.
    • (2009) BMC Genet , vol.10 , pp. 23
    • Millstein, J.1    Zhang, B.2    Zhu, J.3    Schadt, E.E.4
  • 26
    • 84861719484 scopus 로고    scopus 로고
    • Statistical colocalization of monocyte gene expression and genetic risk variants for type 1 diabetes
    • Wallace C, Rotival M, Cooper JD, Rice CM, Yang JH, et al. (2012) Statistical colocalization of monocyte gene expression and genetic risk variants for type 1 diabetes. Hum Mol Genet 21: 2815-2824.
    • (2012) Hum Mol Genet , vol.21 , pp. 2815-2824
    • Wallace, C.1    Rotival, M.2    Cooper, J.D.3    Rice, C.M.4    Yang, J.H.5
  • 27
    • 45549102935 scopus 로고    scopus 로고
    • The transcription factor Erg is essential for definitive hematopoiesis and the function of adult hematopoietic stem cells
    • Loughran SJ, Kruse EA, Hacking DF, de Graaf CA, Hyland CD, et al. (2008) The transcription factor Erg is essential for definitive hematopoiesis and the function of adult hematopoietic stem cells. Nat Immunol 9: 810-819.
    • (2008) Nat Immunol , vol.9 , pp. 810-819
    • Loughran, S.J.1    Kruse, E.A.2    Hacking, D.F.3    de Graaf, C.A.4    Hyland, C.D.5
  • 28
    • 80052729161 scopus 로고    scopus 로고
    • Copy-number variations, noncoding sequences, and human phenotypes
    • Klopocki E, Mundlos S, (2011) Copy-number variations, noncoding sequences, and human phenotypes. Annu Rev Genomics Hum Genet 12: 53-72.
    • (2011) Annu Rev Genomics Hum Genet , vol.12 , pp. 53-72
    • Klopocki, E.1    Mundlos, S.2
  • 29
    • 33644774386 scopus 로고    scopus 로고
    • CRIPak, a novel endogenous Pak1 inhibitor
    • Talukder AH, Meng Q, Kumar R, (2006) CRIPak, a novel endogenous Pak1 inhibitor. Oncogene 25: 1311-1319.
    • (2006) Oncogene , vol.25 , pp. 1311-1319
    • Talukder, A.H.1    Meng, Q.2    Kumar, R.3
  • 30
    • 77950222543 scopus 로고    scopus 로고
    • The challenge of translation in social neuroscience: a review of oxytocin, vasopressin, and affiliative behavior
    • Insel TR, (2010) The challenge of translation in social neuroscience: a review of oxytocin, vasopressin, and affiliative behavior. Neuron 65: 768-779.
    • (2010) Neuron , vol.65 , pp. 768-779
    • Insel, T.R.1
  • 31
    • 84875577737 scopus 로고    scopus 로고
    • Cohort Profile: The 'Children of the 90s'-the index offspring of the Avon Longitudinal Study of Parents and Children
    • Boyd A, Golding J, Macleod J, Lawlor DA, Fraser A, et al. (2012) Cohort Profile: The 'Children of the 90s'-the index offspring of the Avon Longitudinal Study of Parents and Children. Int J Epidemiol 42: 111-147.
    • (2012) Int J Epidemiol , vol.42 , pp. 111-147
    • Boyd, A.1    Golding, J.2    Macleod, J.3    Lawlor, D.A.4    Fraser, A.5
  • 32
    • 0033812249 scopus 로고    scopus 로고
    • A new human genetic resource: a DNA bank established as part of the Avon longitudinal study of pregnancy and childhood (ALSPAC)
    • Jones RW, Ring S, Tyfield L, Hamvas R, Simmons H, et al. (2000) A new human genetic resource: a DNA bank established as part of the Avon longitudinal study of pregnancy and childhood (ALSPAC). Eur J Hum Genet 8: 653-660.
    • (2000) Eur J Hum Genet , vol.8 , pp. 653-660
    • Jones, R.W.1    Ring, S.2    Tyfield, L.3    Hamvas, R.4    Simmons, H.5
  • 33
    • 78649508578 scopus 로고    scopus 로고
    • MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes
    • Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR, (2010) MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol 34: 816-834.
    • (2010) Genet Epidemiol , vol.34 , pp. 816-834
    • Li, Y.1    Willer, C.J.2    Ding, J.3    Scheet, P.4    Abecasis, G.R.5
  • 35
    • 77950461601 scopus 로고    scopus 로고
    • Origins and functional impact of copy number variation in the human genome
    • Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, et al. (2010) Origins and functional impact of copy number variation in the human genome. Nature 464: 704-712.
    • (2010) Nature , vol.464 , pp. 704-712
    • Conrad, D.F.1    Pinto, D.2    Redon, R.3    Feuk, L.4    Gokcumen, O.5
  • 36
    • 84975795680 scopus 로고    scopus 로고
    • An integrated map of genetic variation from 1,092 human genomes
    • Genomes Project C
    • Genomes Project C (2012) Abecasis GR, Auton A, Brooks LD, DePristo MA, et al. (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56-65.
    • (2012) Nature , vol.491 , pp. 56-65
    • Abecasis, G.R.1    Auton, A.2    Brooks, L.D.3    DePristo, M.A.4
  • 38
    • 22844446947 scopus 로고    scopus 로고
    • An integrative genomics approach to infer causal associations between gene expression and disease
    • Schadt EE, Lamb J, Yang X, Zhu J, Edwards S, et al. (2005) An integrative genomics approach to infer causal associations between gene expression and disease. Nat Genet 37: 710-717.
    • (2005) Nat Genet , vol.37 , pp. 710-717
    • Schadt, E.E.1    Lamb, J.2    Yang, X.3    Zhu, J.4    Edwards, S.5
  • 39
    • 45149106353 scopus 로고    scopus 로고
    • Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks
    • Zhu J, Zhang B, Smith EN, Drees B, Brem RB, et al. (2008) Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat Genet 40: 854-861.
    • (2008) Nat Genet , vol.40 , pp. 854-861
    • Zhu, J.1    Zhang, B.2    Smith, E.N.3    Drees, B.4    Brem, R.B.5
  • 40
    • 84879055641 scopus 로고    scopus 로고
    • Passive and active DNA methylation and the interplay with genetic variation in gene regulation
    • Gutierrez-Arcelus M, Lappalainen T, Montgomery SB, Buil A, Ongen H, et al. (2013) Passive and active DNA methylation and the interplay with genetic variation in gene regulation. Elife 2: e00523.
    • (2013) Elife , vol.2
    • Gutierrez-Arcelus, M.1    Lappalainen, T.2    Montgomery, S.B.3    Buil, A.4    Ongen, H.5
  • 41
    • 77955124773 scopus 로고    scopus 로고
    • Learning Bayesian Networks with the bnlearn R Package
    • Scutari M, (2010) Learning Bayesian Networks with the bnlearn R Package. Journal of Statistical Software 35: 1-22.
    • (2010) Journal of Statistical Software , vol.35 , pp. 1-22
    • Scutari, M.1


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