메뉴 건너뛰기




Volumn 2015, Issue , 2015, Pages

The Impact of Normalization Methods on RNA-Seq Data Analysis

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

EID: 84934326250     PISSN: 23146133     EISSN: 23146141     Source Type: Journal    
DOI: 10.1155/2015/621690     Document Type: Article
Times cited : (83)

References (27)
  • 1
    • 84898618335 scopus 로고    scopus 로고
    • Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells
    • S. Zhao, W.-P. Fung-Leung, A. Bittner, K. Ngo, and X. Liu, "Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells", PLoS ONE, vol. 9, no. 1, Article ID e78644, 2014.
    • (2014) PLoS ONE , vol.9 , Issue.1
    • Zhao, S.1    Fung-Leung, W.-P.2    Bittner, A.3    Ngo, K.4    Liu, X.5
  • 2
    • 56549101959 scopus 로고    scopus 로고
    • Alternative isoform regulation in human tissue transcriptomes
    • E. T. Wang, R. Sandberg, S. Luo et al., "Alternative isoform regulation in human tissue transcriptomes", Nature, vol. 456, no. 7221, pp. 470-476, 2008.
    • (2008) Nature , vol.456 , Issue.7221 , pp. 470-476
    • Wang, E.T.1    Sandberg, R.2    Luo, S.3
  • 3
    • 56749098074 scopus 로고    scopus 로고
    • Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
    • Q. Pan, O. Shai, L. J. Lee, B. J. Frey, and B. J. Blencowe, "Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing", Nature Genetics, vol. 40, no. 12, pp. 1413-1415, 2008.
    • (2008) Nature Genetics , vol.40 , Issue.12 , pp. 1413-1415
    • Pan, Q.1    Shai, O.2    Lee, L.J.3    Frey, B.J.4    Blencowe, B.J.5
  • 4
    • 84892599763 scopus 로고    scopus 로고
    • Dispersion estimation and its effect on test performance in RNA-seq data analysis: A simulationbased comparison ofmethods
    • W. M. Landau and P. Liu, "Dispersion estimation and its effect on test performance in RNA-seq data analysis: a simulationbased comparison ofmethods", PLoS ONE, vol. 8, no. 12, Article ID e81415, 2013.
    • (2013) PLoS ONE , vol.8 , Issue.12
    • Landau, W.M.1    Liu, P.2
  • 5
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • A. Mortazavi, B. A. Williams, K. McCue, L. Schaeffer, and B. Wold, "Mapping and quantifying mammalian transcriptomes by RNA-Seq", Nature Methods, vol. 5, no. 7, pp. 621-628, 2008.
    • (2008) Nature Methods , vol.5 , Issue.7 , pp. 621-628
    • Mortazavi, A.1    Williams, B.A.2    McCue, K.3    Schaeffer, L.4    Wold, B.5
  • 6
    • 65649126066 scopus 로고    scopus 로고
    • Transcript length bias in RNAseq data confounds systems biology
    • A. Oshlack and M. J. Wakefield, "Transcript length bias in RNAseq data confounds systems biology", Biology Direct, vol. 4, article 14, 2009.
    • (2009) Biology Direct , vol.4
    • Oshlack, A.1    Wakefield, M.J.2
  • 7
    • 77950460661 scopus 로고    scopus 로고
    • Understanding mechanisms underlying human gene expression variation with RNA sequencing
    • J. K. Pickrell, J. C. Marioni, A. A. Pai et al., "Understanding mechanisms underlying human gene expression variation with RNA sequencing", Nature, vol. 464, no. 7289, pp. 768-772, 2010.
    • (2010) Nature , vol.464 , Issue.7289 , pp. 768-772
    • Pickrell, J.K.1    Marioni, J.C.2    Pai, A.A.3
  • 9
    • 77956873627 scopus 로고    scopus 로고
    • Tackling the widespread and critical impact of batch effects in highthroughput data
    • J. T. Leek, R. B. Scharpf, H. C. Bravo et al., "Tackling the widespread and critical impact of batch effects in highthroughput data", Nature Reviews Genetics, vol. 11, no. 10, pp. 733-739, 2010.
    • (2010) Nature Reviews Genetics , vol.11 , Issue.10 , pp. 733-739
    • Leek, J.T.1    Scharpf, R.B.2    Bravo, H.C.3
  • 10
    • 77949481052 scopus 로고    scopus 로고
    • Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
    • J. H. Bullard, E. Purdom, K. D. Hansen, and S. Dudoit, "Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments", BMC Bioinformatics, vol. 11, article 94, 2010.
    • (2010) BMC Bioinformatics , vol.11
    • Bullard, J.H.1    Purdom, E.2    Hansen, K.D.3    Dudoit, S.4
  • 11
    • 77953176036 scopus 로고    scopus 로고
    • A scaling normalization method for differential expression analysis of RNA-seq data
    • M. D. Robinson and A. Oshlack, "A scaling normalization method for differential expression analysis of RNA-seq data", Genome Biology, vol. 11, no. 3, article r25, 2010.
    • (2010) Genome Biology , vol.11 , Issue.3
    • Robinson, M.D.1    Oshlack, A.2
  • 12
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: A bioconductor package for differential expression analysis of digital gene expression data
    • M. D. Robinson, D. J. McCarthy, and G. K. Smyth, "EdgeR: a bioconductor package for differential expression analysis of digital gene expression data", Bioinformatics, vol. 26, no. 1, pp. 139-140, 2010.
    • (2010) Bioinformatics , vol.26 , Issue.1 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 13
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • S. Anders and W. Huber, "Differential expression analysis for sequence count data", Genome Biology, vol. 11, no. 10, article R106, 2010.
    • (2010) Genome Biology , vol.11 , Issue.10
    • Anders, S.1    Huber, W.2
  • 15
    • 84863562292 scopus 로고    scopus 로고
    • Normalization, testing, and false discovery rate estimation for RNA-sequencing data
    • J. Li, D. M. Witten, I. M. Johnstone, and R. Tibshirani, "Normalization, testing, and false discovery rate estimation for RNA-sequencing data", Biostatistics, vol. 13, no. 3, pp. 523-538, 2012.
    • (2012) Biostatistics , vol.13 , Issue.3 , pp. 523-538
    • Li, J.1    Witten, D.M.2    Johnstone, I.M.3    Tibshirani, R.4
  • 16
    • 84860117771 scopus 로고    scopus 로고
    • Detection of redundant fusion transcripts as biomarkers or disease-specific therapeutic targets in breast cancer
    • Y. W. Asmann, B. M. Necela, K. R. Kalari et al., "Detection of redundant fusion transcripts as biomarkers or disease-specific therapeutic targets in breast cancer", Cancer Research, vol. 72, no. 8, pp. 1921-1928, 2012.
    • (2012) Cancer Research , vol.72 , Issue.8 , pp. 1921-1928
    • Asmann, Y.W.1    Necela, B.M.2    Kalari, K.R.3
  • 17
    • 77957920003 scopus 로고    scopus 로고
    • Polymorphic cisand Trans-Regulation of human gene expression
    • V. G. Cheung, R. R. Nayak, I. X. Wang et al., "Polymorphic cisand Trans-Regulation of human gene expression", PLoS Biology, vol. 8, no. 9, Article IDe1000480, 2010.
    • (2010) PLoS Biology , vol.8 , Issue.9
    • Cheung, V.G.1    Nayak, R.R.2    Wang, I.X.3
  • 18
    • 81055124271 scopus 로고    scopus 로고
    • Recount: A multiexperiment resource of analysis-ready RNA-seq gene count datasets
    • A. C. Frazee, B. Langmead, and J. T. Leek, "Recount: a multiexperiment resource of analysis-ready RNA-seq gene count datasets", BMC Bioinformatics, vol. 12, article 449, 2011.
    • (2011) BMC Bioinformatics , vol.12
    • Frazee, A.C.1    Langmead, B.2    Leek, J.T.3
  • 20
    • 84880396139 scopus 로고    scopus 로고
    • Analysis of boutique arrays: A universal method for the selection of the optimal data normalization procedure
    • B. Uszczynska, J. Zyprych-Walczak, L. Handschuh et al., "Analysis of boutique arrays: a universal method for the selection of the optimal data normalization procedure", International Journal of Molecular Medicine, vol. 32, no. 3, pp. 668-684, 2013.
    • (2013) International Journal of Molecular Medicine , vol.32 , Issue.3 , pp. 668-684
    • Uszczynska, B.1    Zyprych-Walczak, J.2    Handschuh, L.3
  • 22
  • 23
    • 84899949862 scopus 로고    scopus 로고
    • Expression of putative targets of immunotherapy in acute myeloid leukemia and healthy tissues
    • M. Goswami, N. Hensel, B. D. Smith et al., "Expression of putative targets of immunotherapy in acute myeloid leukemia and healthy tissues", Leukemia, vol. 28, no. 5, pp. 1167-1170, 2014.
    • (2014) Leukemia , vol.28 , Issue.5 , pp. 1167-1170
    • Goswami, M.1    Hensel, N.2    Smith, B.D.3
  • 24
    • 84884416048 scopus 로고    scopus 로고
    • Human housekeeping genes, revisited
    • E. Eisenberg and E. Y. Levanon, "Human housekeeping genes, revisited", Trends in Genetics, vol. 29, no. 10, pp. 569-574, 2013.
    • (2013) Trends in Genetics , vol.29 , Issue.10 , pp. 569-574
    • Eisenberg, E.1    Levanon, E.Y.2
  • 25
    • 84928199480 scopus 로고    scopus 로고
    • Comparison of software packages for detecting differential expression in RNAseq studies
    • F. Seyednasrollah, A. Laiho, and L. L. Elo, "Comparison of software packages for detecting differential expression in RNAseq studies", Briefings in Bioinformatics, vol. 16, no. 1, pp. 59-70, 2015.
    • (2015) Briefings in Bioinformatics , vol.16 , Issue.1 , pp. 59-70
    • Seyednasrollah, F.1    Laiho, A.2    Elo, L.L.3
  • 26
    • 84887791432 scopus 로고    scopus 로고
    • A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
    • M.-A. Dillies, A. Rau, J. Aubert et al., "A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis", Briefings in Bioinformatics, vol. 14, no. 6, pp. 671-683, 2013.
    • (2013) Briefings in Bioinformatics , vol.14 , Issue.6 , pp. 671-683
    • Dillies, M.-A.1    Rau, A.2    Aubert, J.3
  • 27
    • 84894069977 scopus 로고    scopus 로고
    • Comparison of normalization methods for differential gene expression analysis in RNA-Seq experiments: A matter of relative size of studied transcriptomes
    • E. Maza, P. Frasse, P. Senin, M. Bouzayen, and M. Zouine, "Comparison of normalization methods for differential gene expression analysis in RNA-Seq experiments: a matter of relative size of studied transcriptomes", Communicative & Integrative Biology, vol. 6, no. 6, Article ID e25849, 2013.
    • (2013) Communicative & Integrative Biology , vol.6 , Issue.6
    • Maza, E.1    Frasse, P.2    Senin, P.3    Bouzayen, M.4    Zouine, M.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.