메뉴 건너뛰기




Volumn 41, Issue 2, 2013, Pages

DiffSplice: The genome-wide detection of differential splicing events with RNA-seq

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; TRANSCRIPTOME;

EID: 84874193712     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1026     Document Type: Article
Times cited : (124)

References (38)
  • 3
    • 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., Frey, B. and Blencowe, B. (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.3    Frey, B.4    Blencowe, B.5
  • 5
    • 34548758543 scopus 로고    scopus 로고
    • Splicing in disease: Disruption of the splicing code and the decoding machinery
    • DOI 10.1038/nrg2164, PII NRG2164
    • Wang, G. and Cooper, T. (2007) Splicing in disease: disruption of the splicing code and the decoding machinery. Nat. Rev. Genet., 8, 749-761. (Pubitemid 47429207)
    • (2007) Nature Reviews Genetics , vol.8 , Issue.10 , pp. 749-761
    • Wang, G.-S.1    Cooper, T.A.2
  • 6
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell, C., Williams, B., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M., Salzberg, S., Wold, B. and Pachter, L. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol., 28, 511-515.
    • (2010) Nat. Biotechnol , vol.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5    Van Baren, M.6    Salzberg, S.7    Wold, B.8    Pachter, L.9
  • 7
    • 0037012922 scopus 로고    scopus 로고
    • Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays
    • DOI 10.1126/science.1069415
    • Clark, T., Sugnet, C. and Ares, M. (2002) Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science, 296, 907-910. (Pubitemid 34464895)
    • (2002) Science , vol.296 , Issue.5569 , pp. 907-910
    • Clark, T.A.1    Sugnet, C.W.2    Ares Jr., M.3
  • 8
    • 40149106038 scopus 로고    scopus 로고
    • Comprehensive analysis of affymetrix exon arrays using bioconductor
    • Okoniewski, M. and Miller, C. (2008) Comprehensive analysis of affymetrix exon arrays using bioconductor. PLoS Comput. Biol., 4, e6.
    • (2008) PLoS Comput. Biol , vol.4
    • Okoniewski, M.1    Miller, C.2
  • 10
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • Wang, Z., Gerstein, M. and Snyder, M. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 10, 57-63.
    • (2009) Nat. Rev. Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 12
    • 78650552020 scopus 로고    scopus 로고
    • Statistical tests for detecting differential RNA-transcript expression from read counts
    • doi:10.1038/npre.2010.4437.1
    • Stegle, O., Drewe, P., Bohnert, R., Borgwardt, K. and Rä tsch, G. (2010) Statistical tests for detecting differential RNA-transcript expression from read counts. Nature Precedings, doi:10.1038/npre.2010.4437.1.
    • (2010) Nature Precedings
    • Stegle, O.1    Drewe, P.2    Bohnert, R.3    Borgwardt, K.4    Rätsch, G.5
  • 13
    • 80053435328 scopus 로고    scopus 로고
    • FDM: A graph-based statistical method to detect differential transcription using RNA-seq data
    • Singh, D., Orellana, C., Hu, Y., Jones, C., Liu, Y., Chiang, D., Liu, J. and Prins, J. (2011) FDM: a graph-based statistical method to detect differential transcription using RNA-seq data. Bioinformatics, 27, 2633-2640.
    • (2011) Bioinformatics , vol.27 , pp. 2633-2640
    • Singh, D.1    Orellana, C.2    Hu, Y.3    Jones, C.4    Liu, Y.5    Chiang, D.6    Liu, J.7    Prins, J.8
  • 15
    • 78649714014 scopus 로고    scopus 로고
    • Analysis and design of RNA sequencing experiments for identifying isoform regulation
    • Katz, Y., Wang, E., Airoldi, E. and Burge, C. (2010) Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat. Methods, 7, 1009-1015.
    • (2010) Nat. Methods , vol.7 , pp. 1009-1015
    • Katz, Y.1    Wang, E.2    Airoldi, E.3    Burge, C.4
  • 16
    • 80054931745 scopus 로고    scopus 로고
    • SpliceTrap: A method to quantify alternative splicing under single cellular conditions
    • Wu, J., Akerman, M., Sun, S., McCombie, W., Krainer, A. and Zhang, M. (2011) SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics, 27, 3010-3016.
    • (2011) Bioinformatics , vol.27 , pp. 3010-3016
    • Wu, J.1    Akerman, M.2    Sun, S.3    McCombie, W.4    Krainer, A.5    Zhang, M.6
  • 17
    • 84860385776 scopus 로고    scopus 로고
    • MATS: A Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data
    • Shen, S., Park, J., Huang, J., Dittmar, K.A., Lu, Z., Zhou, Q., Carstens, R.P. and Xing, Y. (2012) MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. Nucleic Acids Res., 40, e61.
    • (2012) Nucleic Acids Res , vol.40
    • Shen, S.1    Park, J.2    Huang, J.3    Dittmar, K.A.4    Lu, Z.5    Zhou, Q.6    Carstens, R.P.7    Xing, Y.8
  • 19
    • 77955457181 scopus 로고    scopus 로고
    • A probabilistic framework for aligning paired-end RNA-seq data
    • Hu, Y., Wang, K., He, X., Chiang, D., Prins, J. and Liu, J. (2010) A probabilistic framework for aligning paired-end RNA-seq data. Bioinformatics, 26, 1950-1957.
    • (2010) Bioinformatics , vol.26 , pp. 1950-1957
    • Hu, Y.1    Wang, K.2    He, X.3    Chiang, D.4    Prins, J.5    Liu, J.6
  • 24
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • Trapnell, C., Pachter, L. and Salzberg, S. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.3
  • 25
    • 77955443472 scopus 로고    scopus 로고
    • Detection of splice junctions from paired-end RNA-seq data by SpliceMap
    • Au, K., Jiang, H., Lin, L., Xing, Y. and Wong, W. (2010) Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res., 38, 4570-4578.
    • (2010) Nucleic Acids Res , vol.38 , pp. 4570-4578
    • Au, K.1    Jiang, H.2    Lin, L.3    Xing, Y.4    Wong, W.5
  • 29
    • 64549119707 scopus 로고    scopus 로고
    • Statistical inference for isoform expression in RNA-Seq
    • Jiang, H. and Wong, W. (2009) Statistical inference for isoform expression in RNA-Seq. Bioinformatics, 25, 1026-1032.
    • (2009) Bioinformatics , vol.25 , pp. 1026-1032
    • Jiang, H.1    Wong, W.2
  • 30
    • 85052549687 scopus 로고    scopus 로고
    • A two-parameter generalized Poisson model to improve the analysis of RNA-seq data
    • Srivastava, S. and Chen, L. (2010) A two-parameter generalized Poisson model to improve the analysis of RNA-seq data. Nucleic Acids Res., 38, e170.
    • (2010) Nucleic Acids Res , vol.38
    • Srivastava, S.1    Chen, L.2
  • 32
    • 0025952277 scopus 로고
    • Divergence measures based on the shannon entropy
    • doi:10.1109/18.61115
    • Lin, J. (1991) Divergence measures based on the shannon entropy. IEEE Trans. Inf. Theory, 37, 145-151, doi:10.1109/18.61115.
    • (1991) IEEE Trans. Inf. Theory , vol.37 , pp. 145-151
    • Lin, J.1
  • 33
    • 77954302477 scopus 로고    scopus 로고
    • RQuant.web: A tool for RNA-Seq-based transcript quantitation
    • Bohnert, R. and Rä tsch, G. (2010) rQuant.web: a tool for RNA-Seq-based transcript quantitation. Nucleic Acids Res., 38, W348-W351.
    • (2010) Nucleic Acids Res , vol.38
    • Bohnert, R.1    Rätsch, G.2
  • 34
    • 75649089283 scopus 로고    scopus 로고
    • Sequence-non-specific effects of RNA interference triggers and microRNA regulators
    • Olejniczak, M., Galka, P. and Krzyzosiak, W. (2010) Sequence-non-specific effects of RNA interference triggers and microRNA regulators. Nucleic Acids Res., 38, 1-16.
    • (2010) Nucleic Acids Res , vol.38 , pp. 1-16
    • Olejniczak, M.1    Galka, P.2    Krzyzosiak, W.3
  • 35
    • 79952709611 scopus 로고    scopus 로고
    • Improving RNA-Seq expression estimates by correcting for fragment bias
    • Roberts, A., Trapnell, C., Donaghey, J., Rinn, J. and Pachter, L. (2011) Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol., 12, R22.
    • (2011) Genome Biol , vol.12
    • Roberts, A.1    Trapnell, C.2    Donaghey, J.3    Rinn, J.4    Pachter, L.5
  • 36
    • 70249096642 scopus 로고    scopus 로고
    • ErbB4 splice variants cyt1 and cyt2 differ by 16 amino acids and exert opposing effects on the mammary epithelium in vivo
    • Muraoka-Cook, R., Sandahl, M., Strunk, K., Miraglia, L., Husted, C., Hunter, D., Elenius, K., Chodosh, L. and Earp, H.S. (2009) ErbB4 Splice Variants Cyt1 and Cyt2 Differ by 16 Amino Acids and Exert Opposing Effects on the Mammary Epithelium In Vivo. Mol Cell Biol., 29, 4935-4948.
    • (2009) Mol Cell Biol , vol.29 , pp. 4935-4948
    • Muraoka-Cook, R.1    Sandahl, M.2    Strunk, K.3    Miraglia, L.4    Husted, C.5    Hunter, D.6    Elenius, K.7    Chodosh, L.8    Earp, H.S.9
  • 37
    • 0345701306 scopus 로고    scopus 로고
    • A peptide encoded by exon 6 of VEGF (EG3306) inhibits VEGF-induced angiogenesis in vitro and ischaemic retinal neovascularisation in vivo
    • DOI 10.1016/S0006-291X(03)00222-5
    • Bainbridge, J., Jia, H., Bagherzadeh, A., Selwood, D., Ali, R. and Zachary, I. (2003) A peptide encoded by exon 6 of VEGF (EG3306) inhibits VEGF-induced angiogenesis in vitro and ischaemic retinal neovascularisation in vivo. Biochem. Biophys. Res. Commun., 302, 793-799. (Pubitemid 36294043)
    • (2003) Biochemical and Biophysical Research Communications , vol.302 , Issue.4 , pp. 793-799
    • Bainbridge, J.W.B.1    Jia, H.2    Bagherzadeh, A.3    Selwood, D.4    Ali, R.R.5    Zachary, I.6
  • 38
    • 79952227361 scopus 로고    scopus 로고
    • CD44 splice isoform switching in human and mouse epithelium is essential for epithelialmesenchymal transition and breast cancer progression
    • Brown, R., Reinke, L., Damerow, M., Perez, D., Chodosh, L., Yang, J. and Cheng, C. (2011) CD44 splice isoform switching in human and mouse epithelium is essential for epithelialmesenchymal transition and breast cancer progression. J. Clin. Invest., 121, 1064-1074.
    • (2011) J. Clin. Invest , vol.121 , pp. 1064-1074
    • Brown, R.1    Reinke, L.2    Damerow, M.3    Perez, D.4    Chodosh, L.5    Yang, J.6    Cheng, C.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.