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Volumn 45, Issue 5, 2017, Pages

IDP-ASE: Haplotyping and quantifying allele-specific expression at the gene and gene isoform level by hybrid sequencing

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME; MESSENGER RNA; RNA ISOFORM;

EID: 85018322845     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw1076     Document Type: Article
Times cited : (40)

References (47)
  • 1
    • 15244353967 scopus 로고    scopus 로고
    • X-inactivation profile reveals extensive variability in X-linked gene expression in females
    • Carrel, L. and Willard, H.F. (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
  • 4
    • 84861234288 scopus 로고    scopus 로고
    • Mechanisms and consequences of widespread random monoallelic expression
    • Chess, A. (2012) Mechanisms and consequences of widespread random monoallelic expression. Nat. Rev. Genet., 13, 421-428.
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 421-428
    • Chess, A.1
  • 5
    • 1242271304 scopus 로고    scopus 로고
    • Allele-specific gene expression uncovered
    • Knight, J.C. (2004) Allele-specific gene expression uncovered. Trends Genet., 20, 113-116.
    • (2004) Trends Genet. , vol.20 , pp. 113-116
    • Knight, J.C.1
  • 6
    • 79751531332 scopus 로고    scopus 로고
    • Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads
    • Turro, E., Su, S.Y., Goncalves, A., Coin, L.J.M., Richardson, S. and Lewin, A. (2011) Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads. Genome Biol., 12, R13.
    • (2011) Genome Biol. , vol.12 , pp. R13
    • Turro, E.1    Su, S.Y.2    Goncalves, A.3    Coin, L.J.M.4    Richardson, S.5    Lewin, A.6
  • 7
    • 84906994092 scopus 로고    scopus 로고
    • Known unknowns for allele-specific expression and genomic imprinting effects
    • Gregg, C. (2014) Known unknowns for allele-specific expression and genomic imprinting effects. F1000Prime Rep., 6, 75.
    • (2014) F1000Prime Rep. , vol.6 , pp. 75
    • Gregg, C.1
  • 10
    • 84942945203 scopus 로고    scopus 로고
    • Genomic approaches for understanding the genetics of complex disease
    • Lowe, W.L. and Reddy, T.E. (2015) Genomic approaches for understanding the genetics of complex disease. Genome Res., 25, 1432-1441.
    • (2015) Genome Res. , vol.25 , pp. 1432-1441
    • Lowe, W.L.1    Reddy, T.E.2
  • 15
    • 36249017308 scopus 로고    scopus 로고
    • Widespread monoallelic expression on human autosomes
    • Gimelbrant, A., Hutchinson, J.N., Thompson, B.R. and Chess, A. (2007) Widespread monoallelic expression on human autosomes. Science, 318, 1136-1140.
    • (2007) Science , vol.318 , pp. 1136-1140
    • Gimelbrant, A.1    Hutchinson, J.N.2    Thompson, B.R.3    Chess, A.4
  • 16
    • 73649113113 scopus 로고    scopus 로고
    • A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells
    • Lee, J.H., Park, I.H., Gao, Y., Li, J.B., Li, Z., Daley, G.Q., Zhang, K. and Church, G.M. (2009) A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells. PLoS Genet., 5, e1000718.
    • (2009) PLoS Genet. , vol.5 , pp. e1000718
    • Lee, J.H.1    Park, I.H.2    Gao, Y.3    Li, J.B.4    Li, Z.5    Daley, G.Q.6    Zhang, K.7    Church, G.M.8
  • 17
    • 68349089152 scopus 로고    scopus 로고
    • Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human
    • Zhang, K., Li, J.B., Gao, Y., Egli, D., Xie, B., Deng, J., Li, Z., Lee, J.H., Aach, J., Leproust, E.M. et al. (2009) Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. Nat. Methods, 6, U613-U690.
    • (2009) Nat. Methods , vol.6 , pp. U613-U690
    • Zhang, K.1    Li, J.B.2    Gao, Y.3    Egli, D.4    Xie, B.5    Deng, J.6    Li, Z.7    Lee, J.H.8    Aach, J.9    Leproust, E.M.10
  • 18
    • 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. 533-538
    • Pastinen, T.1
  • 20
    • 84856753476 scopus 로고    scopus 로고
    • A statistical framework for eQTL mapping using RNA-seq data
    • Sun, W. (2012) A statistical framework for eQTL mapping using RNA-seq data. Biometrics, 68, 1-11.
    • (2012) Biometrics , vol.68 , pp. 1-11
    • Sun, W.1
  • 21
    • 84879419235 scopus 로고    scopus 로고
    • Allelic imbalance metre (Allim), a new tool for measuring allele-specific gene expression with RNA-seq data
    • Pandey, R.V., Franssen, S.U., Futschik, A. and Schlotterer, C. (2013) Allelic imbalance metre (Allim), a new tool for measuring allele-specific gene expression with RNA-seq data. Mol. Ecol. Resour., 13, 740-745.
    • (2013) Mol. Ecol. Resour. , vol.13 , pp. 740-745
    • Pandey, R.V.1    Franssen, S.U.2    Futschik, A.3    Schlotterer, C.4
  • 22
    • 84919904506 scopus 로고    scopus 로고
    • Allele Workbench: Transcriptome pipeline and interactive graphics for allele-specific expression
    • Soderlund, C.A., Nelson, W.M. and Goff, S.A. (2014) Allele Workbench: Transcriptome pipeline and interactive graphics for allele-specific expression. PLoS One, 9, e115740.
    • (2014) PLoS One , vol.9 , pp. e115740
    • Soderlund, C.A.1    Nelson, W.M.2    Goff, S.A.3
  • 24
    • 84928166234 scopus 로고    scopus 로고
    • ASEQ: Fast allele-specific studies from next-generation sequencing data
    • Romanel, A., Lago, S., Prandi, D., Sboner, A. and Demichelis, F. (2015) ASEQ: Fast allele-specific studies from next-generation sequencing data. BMC Med. Genomics, 8, 9.
    • (2015) BMC Med. Genomics , vol.8 , pp. 9
    • Romanel, A.1    Lago, S.2    Prandi, D.3    Sboner, A.4    Demichelis, F.5
  • 25
    • 84924388025 scopus 로고    scopus 로고
    • PRDM9 drives evolutionary erosion of hotspots in Mus musculus through haplotype-specific initiation of meiotic recombination
    • Baker, C.L., Kajita, S., Walker, M., Saxl, R.L., Raghupathy, N., Choi, K., Petkov, P.M. and Paigen, K. (2015) PRDM9 drives evolutionary erosion of hotspots in Mus musculus through haplotype-specific initiation of meiotic recombination. PLoS Genet., 11, e1004916.
    • (2015) PLoS Genet. , vol.11 , pp. e1004916
    • Baker, C.L.1    Kajita, S.2    Walker, M.3    Saxl, R.L.4    Raghupathy, N.5    Choi, K.6    Petkov, P.M.7    Paigen, K.8
  • 26
    • 84907543218 scopus 로고    scopus 로고
    • Estimates of allele-specific expression in Drosophila with a single genome sequence and RNA-seq data
    • Quinn, A., Juneja, P. and Jiggins, F.M. (2014) Estimates of allele-specific expression in Drosophila with a single genome sequence and RNA-seq data. Bioinformatics, 30, 2603-2610.
    • (2014) Bioinformatics , vol.30 , pp. 2603-2610
    • Quinn, A.1    Juneja, P.2    Jiggins, F.M.3
  • 27
    • 80053522581 scopus 로고    scopus 로고
    • A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data
    • Skelly, D.A., Johansson, M., Madeoy, J., Wakefield, J. and Akey, J.M. (2011) A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data. Genome Res., 21, 1728-1737.
    • (2011) Genome Res. , vol.21 , pp. 1728-1737
    • Skelly, D.A.1    Johansson, M.2    Madeoy, J.3    Wakefield, J.4    Akey, J.M.5
  • 32
    • 84887412533 scopus 로고    scopus 로고
    • A single-molecule long-read survey of the human transcriptome
    • Sharon, D., Tilgner, H., Grubert, F. and Snyder, M. (2013) A single-molecule long-read survey of the human transcriptome. Nat. Biotechnol., 31, 1009-1014.
    • (2013) Nat. Biotechnol. , vol.31 , pp. 1009-1014
    • Sharon, D.1    Tilgner, H.2    Grubert, F.3    Snyder, M.4
  • 33
    • 84904016056 scopus 로고    scopus 로고
    • Defining a personal, allele-specific, and single-molecule long-read transcriptome
    • Tilgner, H., Grubert, F., Sharon, D. and Snyder, M.P. (2014) Defining a personal, allele-specific, and single-molecule long-read transcriptome. Proc. Natl. Acad. Sci. U.S.A., 111, 9869-9874.
    • (2014) Proc. Natl. Acad. Sci. U.S.A. , vol.111 , pp. 9869-9874
    • Tilgner, H.1    Grubert, F.2    Sharon, D.3    Snyder, M.P.4
  • 35
    • 84867121279 scopus 로고    scopus 로고
    • Improving PacBio long read accuracy by short read alignment
    • Au, K.F., Underwood, J.G., Lee, L. and Wong, W.H. (2012) Improving PacBio long read accuracy by short read alignment. PLoS One, 7, e46679.
    • (2012) PLoS One , vol.7 , pp. e46679
    • Au, K.F.1    Underwood, J.G.2    Lee, L.3    Wong, W.H.4
  • 39
    • 1642370803 scopus 로고    scopus 로고
    • Slice sampling
    • Neal, R.M. (2003) Slice sampling. Ann. Stat., 31, 705-741.
    • (2003) Ann. Stat. , vol.31 , pp. 705-741
    • Neal, R.M.1
  • 40
    • 48949103013 scopus 로고    scopus 로고
    • An MCMC algorithm for haplotype assembly from whole-genome sequence data
    • Bansal, V., Halpern, A.L., Axelrod, N. and Bafna, V. (2008) An MCMC algorithm for haplotype assembly from whole-genome sequence data. Genome Res., 18, 1336-1346.
    • (2008) Genome Res. , vol.18 , pp. 1336-1346
    • Bansal, V.1    Halpern, A.L.2    Axelrod, N.3    Bafna, V.4
  • 41
    • 64549119707 scopus 로고    scopus 로고
    • Statistical inferences for isoform expression in RNA-Seq
    • Jiang, H. and Wong, W.H. (2009) Statistical inferences for isoform expression in RNA-Seq. Bioinformatics, 25, 1026-1032.
    • (2009) Bioinformatics , vol.25 , pp. 1026-1032
    • Jiang, H.1    Wong, W.H.2
  • 47
    • 36448996703 scopus 로고    scopus 로고
    • Breast cancer risk associated with BRCA1 and BRCA2 in diverse populations
    • Fackenthal, J.D. and Olopade, O.I. (2007) Breast cancer risk associated with BRCA1 and BRCA2 in diverse populations. Nat. Rev. Cancer, 7, 937-948.
    • (2007) Nat. Rev. Cancer , vol.7 , pp. 937-948
    • Fackenthal, J.D.1    Olopade, O.I.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.