메뉴 건너뛰기




Volumn 38, Issue 10, 2010, Pages

Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE RNA SPLICING; ARTICLE; COMPUTER PREDICTION; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; DNA MICROARRAY; EXON; GENE EXPRESSION; HUMAN; HUMAN CELL; HUMAN GENETICS; INTERMETHOD COMPARISON; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RNA SEQUENCE; SENSITIVITY ANALYSIS; SEQUENCE DATABASE; STATISTICAL MODEL; VALIDATION PROCESS; CELL LINE; COMPUTER SIMULATION; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; SEQUENCE ANALYSIS; VALIDATION STUDY;

EID: 77954127002     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq041     Document Type: Article
Times cited : (124)

References (53)
  • 2
    • 0037062982 scopus 로고    scopus 로고
    • Alternative pre-mRNA splicing and proteome expansion in metazoans
    • Maniatis,T. and Tasic,B. (2002) Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature, 418, 236-243.
    • (2002) Nature , vol.418 , pp. 236-243
    • Maniatis, T.1    Tasic, B.2
  • 3
    • 41149149041 scopus 로고    scopus 로고
    • The functional consequences of alternative promoter use in mammalian genomes
    • Davuluri,R.V., Suzuki,Y., Sugano,S., Plass,C. and Huang,T.H. (2008) The functional consequences of alternative promoter use in mammalian genomes. Trends Genet., 24, 167-177.
    • (2008) Trends Genet , vol.24 , pp. 167-177
    • Davuluri, R.V.1    Suzuki, Y.2    Sugano, S.3    Plass, C.4    Huang, T.H.5
  • 4
    • 33646950851 scopus 로고    scopus 로고
    • Biased alternative polyadenylation in human tissues
    • Zhang,H., Lee,J.Y. and Tian,B. (2005) Biased alternative polyadenylation in human tissues. Genome Biol., 6, R100.
    • (2005) Genome Biol , vol.6
    • Zhang, H.1    Lee, J.Y.2    Tian, B.3
  • 5
    • 55749105893 scopus 로고    scopus 로고
    • Alternative splicing and the progesterone receptor in breast cancer
    • Cork,D., Lennard,T. and Tyson-Capper,A. (2008) Alternative splicing and the progesterone receptor in breast cancer. Breast Cancer Res., 10, 207.
    • (2008) Breast Cancer Res , vol.10 , pp. 207
    • Cork, D.1    Lennard, T.2    Tyson-Capper, A.3
  • 9
    • 56749098074 scopus 로고    scopus 로고
    • Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
    • Pan,Q., Shai,O., Lee,L.J., Frey,B.J. and Blencowe,B.J. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet., 40, 1413-1415.
    • (2008) Nat. Genet. , vol.40 , pp. 1413-1415
    • Pan, Q.1    Shai, O.2    Lee, L.J.3    Frey, B.J.4    Blencowe, B.J.5
  • 11
    • 4444270781 scopus 로고    scopus 로고
    • Genome wide identification and classification of alternative splicing based on EST data
    • Gupta,S., Zink,D., Korn,B., Vingron,M. and Haas,S.A. (2004) Genome wide identification and classification of alternative splicing based on EST data. Bioinformatics, 20, 2579-2585.
    • (2004) Bioinformatics , vol.20 , pp. 2579-2585
    • Gupta, S.1    Zink, D.2    Korn, B.3    Vingron, M.4    Haas, S.A.5
  • 12
    • 17244377195 scopus 로고    scopus 로고
    • Bioinformatics analysis of alternative splicing
    • Lee,C. and Wang,Q. (2005) Bioinformatics analysis of alternative splicing. Brief. Bioinform., 6, 23-33.
    • (2005) Brief. Bioinform. , vol.6 , pp. 23-33
    • Lee, C.1    Wang, Q.2
  • 13
    • 33745156134 scopus 로고    scopus 로고
    • An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs
    • Xing,Y., Yu,T., Wu,Y.N., Roy,M., Kim,J. and Lee,C. (2006) An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs. Nucleic Acids Res., 34, 3150-3160.
    • (2006) Nucleic Acids Res , vol.34 , pp. 3150-3160
    • Xing, Y.1    Yu, T.2    Wu, Y.N.3    Roy, M.4    Kim, J.5    Lee, C.6
  • 14
    • 4344641894 scopus 로고    scopus 로고
    • Analysis of alternative splicing with microarrays: successes and challenges
    • Lee,C. and Roy,M. (2004) Analysis of alternative splicing with microarrays: successes and challenges. Genome Biol., 5, 231.
    • (2004) Genome Biol , vol.5 , pp. 231
    • Lee, C.1    Roy, M.2
  • 15
    • 33745899048 scopus 로고    scopus 로고
    • Alternative splicing: new insights from global analyses
    • Blencowe,B.J. (2006) Alternative splicing: new insights from global analyses. Cell, 126, 37-47.
    • (2006) Cell , vol.126 , pp. 37-47
    • Blencowe, B.J.1
  • 16
    • 0037012922 scopus 로고    scopus 로고
    • Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays
    • Clark,T.A., Sugnet,C.W. and Ares,M. (2002) Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science, 296, 907-910.
    • (2002) Science , vol.296 , pp. 907-910
    • Clark, T.A.1    Sugnet, C.W.2    Ares, M.3
  • 17
    • 16544378889 scopus 로고    scopus 로고
    • Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data
    • Le,K., Mitsouras,K., Roy,M., Wang,Q., Xu,Q., Nelson,S.F. and Lee,C. (2004) Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data. Nucleic Acids Res., 32, e180.
    • (2004) Nucleic Acids Res , vol.32
    • Le, K.1    Mitsouras, K.2    Roy, M.3    Wang, Q.4    Xu, Q.5    Nelson, S.F.6    Lee, C.7
  • 22
    • 48149096726 scopus 로고    scopus 로고
    • MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays
    • Xing,Y., Stoilov,P., Kapur,K., Han,A., Jiang,H., Shen,S., Black,D.L. and Wong,W.H. (2008) MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays. RNA., 14, 1470-1479.
    • (2008) RNA , vol.14 , pp. 1470-1479
    • Xing, Y.1    Stoilov, P.2    Kapur, K.3    Han, A.4    Jiang, H.5    Shen, S.6    Black, D.L.7    Wong, W.H.8
  • 24
    • 50649089207 scopus 로고    scopus 로고
    • RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays
    • Marioni,J., Mason,C., Mane,S., Stephens,M. and Gilad,Y. (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res., 18, 1509-1517.
    • (2008) Genome Res , vol.18 , pp. 1509-1517
    • Marioni, J.1    Mason, C.2    Mane, S.3    Stephens, M.4    Gilad, Y.5
  • 26
    • 45549088326 scopus 로고    scopus 로고
    • The transcriptional landscape of the yeast genome defined by RNA sequencing
    • Nagalakshmi,U., Wang,Z., Waern,K., Shou,C., Raha,D., Gerstein,M. and Snyder,M. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science, 320, 1344-1349.
    • (2008) Science , vol.320 , pp. 1344-1349
    • Nagalakshmi, U.1    Wang, Z.2    Waern, K.3    Shou, C.4    Raha, D.5    Gerstein, M.6    Snyder, M.7
  • 30
    • 58149490714 scopus 로고    scopus 로고
    • Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model
    • Li,H., Lovci,M.T., Kwon,Y.S., Rosenfeld,M.G., Fu,X.D. and Yeo,G.W. (2008) Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model. Proc. Natl Acad. Sci. USA, 105, 20179-20184.
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 20179-20184
    • Li, H.1    Lovci, M.T.2    Kwon, Y.S.3    Rosenfeld, M.G.4    Fu, X.D.5    Yeo, G.W.6
  • 32
    • 0030681260 scopus 로고    scopus 로고
    • The significance of digital gene expression profiles
    • Audic,S. and Claverie,J.M. (1997) The significance of digital gene expression profiles. Genome Res., 7, 986-995.
    • (1997) Genome Res , vol.7 , pp. 986-995
    • Audic, S.1    Claverie, J.M.2
  • 34
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini,Y. and Hochberg,Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Statist. Soc. B, 57, 289-300.
    • (1995) J. R. Statist. Soc. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 36
    • 52649157765 scopus 로고    scopus 로고
    • Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
    • Dohm,J.C., Lottaz,C., Borodina,T. and Himmelbauer,H. (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res., 36, e105.
    • (2008) Nucleic Acids Res , vol.36
    • Dohm, J.C.1    Lottaz, C.2    Borodina, T.3    Himmelbauer, H.4
  • 37
    • 0034333112 scopus 로고    scopus 로고
    • GeneNest: automated generation and visualization of gene indices
    • Haas,S.A., Beissbarth,T., Rivals,E., Krause,A. and Vingron,M. (2000) GeneNest: automated generation and visualization of gene indices. Trends Genet., 16, 521-523.
    • (2000) Trends Genet , vol.16 , pp. 521-523
    • Haas, S.A.1    Beissbarth, T.2    Rivals, E.3    Krause, A.4    Vingron, M.5
  • 38
    • 0141940266 scopus 로고    scopus 로고
    • Genome-scale design of PCR primers and long oligomers for DNA microarrays
    • Haas,S.A., Hild,M., Wright,A.P., Hain,T., Talibi,D. and Vingron,M. (2003) Genome-scale design of PCR primers and long oligomers for DNA microarrays. Nucleic Acids Res., 31, 5576-5581.
    • (2003) Nucleic Acids Res , vol.31 , pp. 5576-5581
    • Haas, S.A.1    Hild, M.2    Wright, A.P.3    Hain, T.4    Talibi, D.5    Vingron, M.6
  • 40
    • 34548853750 scopus 로고    scopus 로고
    • Exon arrays provide accurate assessments of gene expression
    • Kapur,K., Xing,Y., Ouyang,Z. and Wong,W.H. (2007) Exon arrays provide accurate assessments of gene expression. Genome Biol., 8, R82.
    • (2007) Genome Biol , vol.8
    • Kapur, K.1    Xing, Y.2    Ouyang, Z.3    Wong, W.H.4
  • 45
    • 46249092601 scopus 로고    scopus 로고
    • Proliferating cells express mRNAs with shortened 30 untranslated regions and fewer microRNA target sites
    • Sandberg,R., Neilson,J.R., Sarma,A., Sharp,P.A. and Burge,C.B. (2008) Proliferating cells express mRNAs with shortened 30 untranslated regions and fewer microRNA target sites. Science, 320, 1643-1647.
    • (2008) Science , vol.320 , pp. 1643-1647
    • Sandberg, R.1    Neilson, J.R.2    Sarma, A.3    Sharp, P.A.4    Burge, C.B.5
  • 48
    • 0345647074 scopus 로고    scopus 로고
    • Characterization of myocyte enhancer factor 2 (MEF2) expression in B and T cells: MEF2C is a B cell-restricted transcription factor in lymphocytes
    • Swanson,B.J., Jack,H.M. and Lyons,G.E. (1998) Characterization of myocyte enhancer factor 2 (MEF2) expression in B and T cells: MEF2C is a B cell-restricted transcription factor in lymphocytes. Mol. Immunol., 35, 445-458.
    • (1998) Mol. Immunol. , vol.35 , pp. 445-458
    • Swanson, B.J.1    Jack, H.M.2    Lyons, G.E.3
  • 49
    • 27244443082 scopus 로고    scopus 로고
    • Proliferation marker Ki-67 in early breast cancer
    • Urruticoechea,A., Smith,I.E. and Dowsett,M. (2005) Proliferation marker Ki-67 in early breast cancer. J. Clin. Oncol., 23, 7212-7220.
    • (2005) J. Clin. Oncol. , vol.23 , pp. 7212-7220
    • Urruticoechea, A.1    Smith, I.E.2    Dowsett, M.3
  • 53
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.