메뉴 건너뛰기




Volumn 7, Issue 6, 2012, Pages

Genotype-based test in mapping Cis-regulatory variants from Allele-specific expression data

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

EID: 84862017684     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0038667     Document Type: Article
Times cited : (6)

References (45)
  • 1
    • 0016669094 scopus 로고
    • Evolution at two levels in humans and chimpanzees
    • King MC, Wilson AC, (1975) Evolution at two levels in humans and chimpanzees. Science 188: 107 116.
    • (1975) Science , vol.188 , pp. 107
    • King, M.C.1    Wilson, A.C.2
  • 2
    • 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, (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
    • Hindorff, L.A.1    Sethupathy, P.2    Junkins, H.A.3    Ramos, E.M.4    Mehta, J.P.5
  • 5
    • 73349126396 scopus 로고    scopus 로고
    • Geographical genomics of human leukocyte gene expression variation in southern Morocco
    • Idaghdour Y, Czika W, Shianna KV, Lee SH, Visscher PM, (2010) Geographical genomics of human leukocyte gene expression variation in southern Morocco. Nature genetics 42: 62 67.
    • (2010) Nature Genetics , vol.42 , pp. 62
    • Idaghdour, Y.1    Czika, W.2    Shianna, K.V.3    Lee, S.H.4    Visscher, P.M.5
  • 6
    • 70350651269 scopus 로고    scopus 로고
    • Global patterns of cis variation in human cells revealed by high-density allelic expression analysis
    • Ge B, Pokholok DK, Kwan T, Grundberg E, Morcos L, (2009) Global patterns of cis variation in human cells revealed by high-density allelic expression analysis. Nat Genet 41: 1216 1222.
    • (2009) Nat Genet , vol.41 , pp. 1216
    • Ge, B.1    Pokholok, D.K.2    Kwan, T.3    Grundberg, E.4    Morcos, L.5
  • 7
    • 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, (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464: 773 777.
    • (2010) Nature , vol.464 , pp. 773
    • Montgomery, S.B.1    Sammeth, M.2    Gutierrez-Arcelus, M.3    Lach, R.P.4    Ingle, C.5
  • 8
    • 77954763156 scopus 로고    scopus 로고
    • Genome-wide allele-specific analysis: insights into regulatory variation
    • Pastinen T, (2010) Genome-wide allele-specific analysis: insights into regulatory variation. Nat Rev Genet 11: 533 538.
    • (2010) Nat Rev Genet , vol.11 , pp. 533
    • Pastinen, T.1
  • 9
    • 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, (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464: 768 772.
    • (2010) Nature , vol.464 , pp. 768
    • Pickrell, J.K.1    Marioni, J.C.2    Pai, A.A.3    Degner, J.F.4    Engelhardt, B.E.5
  • 11
  • 12
    • 58149357315 scopus 로고    scopus 로고
    • Validating discovered Cis-acting regulatory genetic variants: application of an allele specific expression approach to HapMap populations
    • Campino S, Forton J, Raj S, Mohr B, Auburn S, (2008) Validating discovered Cis-acting regulatory genetic variants: application of an allele specific expression approach to HapMap populations. PLoS ONE 3: e4105.
    • (2008) PLoS ONE , vol.3
    • Campino, S.1    Forton, J.2    Raj, S.3    Mohr, B.4    Auburn, S.5
  • 13
    • 33846010742 scopus 로고    scopus 로고
    • Localization of a long-range cis-regulatory element of IL13 by allelic transcript ratio mapping
    • Forton JT, Udalova IA, Campino S, Rockett KA, Hull J, (2007) Localization of a long-range cis-regulatory element of IL13 by allelic transcript ratio mapping. Genome Res 17: 82 87.
    • (2007) Genome Res , vol.17 , pp. 82
    • Forton, J.T.1    Udalova, I.A.2    Campino, S.3    Rockett, K.A.4    Hull, J.5
  • 14
    • 34247579326 scopus 로고    scopus 로고
    • Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 and modulates expression of PTGER4
    • Libioulle C, Louis E, Hansoul S, Sandor C, Farnir F, (2007) Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 and modulates expression of PTGER4. PLoS Genet 3: e58.
    • (2007) PLoS Genet , vol.3
    • Libioulle, C.1    Louis, E.2    Hansoul, S.3    Sandor, C.4    Farnir, F.5
  • 16
    • 33644974019 scopus 로고    scopus 로고
    • A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase
    • Scheet P, Stephens M, (2006) A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 78: 629 644.
    • (2006) Am J Hum Genet , vol.78 , pp. 629
    • Scheet, P.1    Stephens, M.2
  • 17
    • 0035071957 scopus 로고    scopus 로고
    • A new statistical method for haplotype reconstruction from population data
    • Stephens M, Smith NJ, Donnelly P, (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68: 978 989.
    • (2001) Am J Hum Genet , vol.68 , pp. 978
    • Stephens, M.1    Smith, N.J.2    Donnelly, P.3
  • 19
    • 57749083496 scopus 로고    scopus 로고
    • Regulation of estrogen receptor-mediated long range transcription via evolutionarily conserved distal response elements
    • Pan YF, Wansa KD, Liu MH, Zhao B, Hong SZ, (2008) Regulation of estrogen receptor-mediated long range transcription via evolutionarily conserved distal response elements. J Biol Chem 283: 32977 32988.
    • (2008) J Biol Chem , vol.283 , pp. 32977
    • Pan, Y.F.1    Wansa, K.D.2    Liu, M.H.3    Zhao, B.4    Hong, S.Z.5
  • 22
    • 45849084287 scopus 로고    scopus 로고
    • Fraction of informative recombinations: a heuristic approach to analyze recombination rates
    • Lefebvre JF, Labuda D, (2008) Fraction of informative recombinations: a heuristic approach to analyze recombination rates. Genetics 178: 2069 2079.
    • (2008) Genetics , vol.178 , pp. 2069
    • Lefebvre, J.F.1    Labuda, D.2
  • 24
    • 67651225410 scopus 로고    scopus 로고
    • Sensitive detection of chromosomal segments of distinct ancestry in admixed populations
    • Price AL, Tandon A, Patterson N, Barnes KC, Rafaels N, (2009) Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet 5: e1000519.
    • (2009) PLoS Genet , vol.5
    • Price, A.L.1    Tandon, A.2    Patterson, N.3    Barnes, K.C.4    Rafaels, N.5
  • 25
    • 61449086542 scopus 로고    scopus 로고
    • Shape-IT: new rapid and accurate algorithm for haplotype inference
    • Delaneau O, Coulonges C, Zagury JF, (2008) Shape-IT: new rapid and accurate algorithm for haplotype inference. BMC Bioinformatics 9: 540.
    • (2008) BMC Bioinformatics , vol.9 , pp. 540
    • Delaneau, O.1    Coulonges, C.2    Zagury, J.F.3
  • 26
    • 80053019891 scopus 로고    scopus 로고
    • Haplotype phasing: existing methods and new developments
    • Browning SR, Browning BL, (2011) Haplotype phasing: existing methods and new developments. Nat Rev Genet 12: 703 714.
    • (2011) Nat Rev Genet , vol.12 , pp. 703
    • Browning, S.R.1    Browning, B.L.2
  • 27
  • 28
    • 40149090710 scopus 로고    scopus 로고
    • Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression
    • Serre D, Gurd S, Ge B, Sladek R, Sinnett D, (2008) Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression. PLoS Genet 4: e1000006.
    • (2008) PLoS Genet , vol.4
    • Serre, D.1    Gurd, S.2    Ge, B.3    Sladek, R.4    Sinnett, D.5
  • 29
    • 67349208839 scopus 로고    scopus 로고
    • Genome-wide association study of blood pressure and hypertension
    • Levy D, Ehret GB, Rice K, Verwoert GC, Launer LJ, (2009) Genome-wide association study of blood pressure and hypertension. Nat Genet 41: 677 687.
    • (2009) Nat Genet , vol.41 , pp. 677
    • Levy, D.1    Ehret, G.B.2    Rice, K.3    Verwoert, G.C.4    Launer, L.J.5
  • 30
    • 34548805282 scopus 로고    scopus 로고
    • A genome-wide association study of global gene expression
    • Dixon AL, Liang L, Moffatt MF, Chen W, Heath S, (2007) A genome-wide association study of global gene expression. Nat Genet 39: 1202 1207.
    • (2007) Nat Genet , vol.39 , pp. 1202
    • Dixon, A.L.1    Liang, L.2    Moffatt, M.F.3    Chen, W.4    Heath, S.5
  • 32
    • 68149100807 scopus 로고    scopus 로고
    • Genome-wide association study identifies variants at 9p21 and 22q13 associated with development of cutaneous nevi
    • Falchi M, Bataille V, Hayward NK, Duffy DL, Bishop JA, (2009) Genome-wide association study identifies variants at 9p21 and 22q13 associated with development of cutaneous nevi. Nat Genet 41: 915 919.
    • (2009) Nat Genet , vol.41 , pp. 915
    • Falchi, M.1    Bataille, V.2    Hayward, N.K.3    Duffy, D.L.4    Bishop, J.A.5
  • 33
    • 58049200536 scopus 로고    scopus 로고
    • Genome-wide association study implicates a chromosome 12 risk locus for late-onset Alzheimer disease
    • Beecham GW, Martin ER, Li YJ, Slifer MA, Gilbert JR, (2009) Genome-wide association study implicates a chromosome 12 risk locus for late-onset Alzheimer disease. Am J Hum Genet 84: 35 43.
    • (2009) Am J Hum Genet , vol.84 , pp. 35
    • Beecham, G.W.1    Martin, E.R.2    Li, Y.J.3    Slifer, M.A.4    Gilbert, J.R.5
  • 34
    • 62449323766 scopus 로고    scopus 로고
    • Genetic variation in the lymphotoxin-alpha pathway and the risk of ischemic stroke in European populations
    • Freilinger T, Bevan S, Ripke S, Gschwendtner A, Lichtner P, (2009) Genetic variation in the lymphotoxin-alpha pathway and the risk of ischemic stroke in European populations. Stroke 40: 970 972.
    • (2009) Stroke , vol.40 , pp. 970
    • Freilinger, T.1    Bevan, S.2    Ripke, S.3    Gschwendtner, A.4    Lichtner, P.5
  • 35
    • 59049108326 scopus 로고    scopus 로고
    • Association between a pro-inflammatory genetic profile and the risk of chronic atrophic gastritis among older adults from Germany
    • Gao L, Weck MN, Nieters A, Brenner H, (2009) Association between a pro-inflammatory genetic profile and the risk of chronic atrophic gastritis among older adults from Germany. Eur J Cancer 45: 428 434.
    • (2009) Eur J Cancer , vol.45 , pp. 428
    • Gao, L.1    Weck, M.N.2    Nieters, A.3    Brenner, H.4
  • 36
    • 65449169623 scopus 로고    scopus 로고
    • Common gene variants in the tumor necrosis factor (TNF) and TNF receptor superfamilies and NF-kB transcription factors and non-Hodgkin lymphoma risk
    • Wang SS, Purdue MP, Cerhan JR, Zheng T, Menashe I, (2009) Common gene variants in the tumor necrosis factor (TNF) and TNF receptor superfamilies and NF-kB transcription factors and non-Hodgkin lymphoma risk. PLoS ONE 4: e5360.
    • (2009) PLoS ONE , vol.4
    • Wang, S.S.1    Purdue, M.P.2    Cerhan, J.R.3    Zheng, T.4    Menashe, I.5
  • 37
    • 45149108420 scopus 로고    scopus 로고
    • Mapping the genetic architecture of gene expression in human liver
    • Schadt EE, Molony C, Chudin E, Hao K, Yang X, (2008) Mapping the genetic architecture of gene expression in human liver. PLoS Biol 6: e107.
    • (2008) PLoS Biol , vol.6
    • Schadt, E.E.1    Molony, C.2    Chudin, E.3    Hao, K.4    Yang, X.5
  • 40
    • 77950854479 scopus 로고    scopus 로고
    • Heritable individual-specific and allele-specific chromatin signatures in humans
    • McDaniell R, Lee BK, Song L, Liu Z, Boyle AP, (2010) Heritable individual-specific and allele-specific chromatin signatures in humans. Science 328: 235 239.
    • (2010) Science , vol.328 , pp. 235
    • McDaniell, R.1    Lee, B.K.2    Song, L.3    Liu, Z.4    Boyle, A.P.5
  • 41
    • 0036184745 scopus 로고    scopus 로고
    • Generating samples under a Wright-Fisher neutral model of genetic variation
    • Hudson RR, (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337 338.
    • (2002) Bioinformatics , vol.18 , pp. 337
    • Hudson, R.R.1
  • 42
    • 33847273741 scopus 로고    scopus 로고
    • msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots
    • Hellenthal G, Stephens M, (2007) msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots. Bioinformatics 23: 520 521.
    • (2007) Bioinformatics , vol.23 , pp. 520
    • Hellenthal, G.1    Stephens, M.2
  • 43
    • 0023796209 scopus 로고
    • On measures of gametic disequilibrium
    • Lewontin RC, (1988) On measures of gametic disequilibrium. Genetics 120: 849 852.
    • (1988) Genetics , vol.120 , pp. 849
    • Lewontin, R.C.1
  • 44
    • 78049259700 scopus 로고    scopus 로고
    • Computational analysis of whole-genome differential allelic expression data in human
    • Wagner JR, Ge B, Pokholok D, Gunderson KL, Pastinen T, (2010) Computational analysis of whole-genome differential allelic expression data in human. PLoS Comput Biol 6: e1000849.
    • (2010) PLoS Comput Biol , vol.6
    • Wagner, J.R.1    Ge, B.2    Pokholok, D.3    Gunderson, K.L.4    Pastinen, T.5
  • 45
    • 58149163446 scopus 로고    scopus 로고
    • Tissue-specific genetic control of splicing: implications for the study of complex traits
    • Heinzen EL, Ge D, Cronin KD, Maia JM, Shianna KV, (2008) Tissue-specific genetic control of splicing: implications for the study of complex traits. PLoS Biol 6: e1.
    • (2008) PLoS Biol , vol.6
    • Heinzen, E.L.1    Ge, D.2    Cronin, K.D.3    Maia, J.M.4    Shianna, K.V.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.