메뉴 건너뛰기




Volumn 15, Issue 8, 2014, Pages

Bootstrap-based differential gene expression analysis for RNA-Seq data with and without replicates

Author keywords

Bootstrapping; Differential gene expression; RNA Seq

Indexed keywords

BOOTSTRAPPING; GENE EXPRESSION; RUNNING; STATISTICAL MODEL; BIOLOGY; COMPUTER PROGRAM; GENE EXPRESSION PROFILING; GENETIC DATABASE; PROCEDURES; SEQUENCE ANALYSIS;

EID: 84965185536     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-S8-S2     Document Type: Article
Times cited : (42)

References (21)
  • 1
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-seq
    • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNA-seq. Nature methods. 2008, 5 (7): 621-628. 10.1038/nmeth.1226.
    • (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
  • 2
    • 70350218818 scopus 로고    scopus 로고
    • Applications of new sequencing technologies for transcriptome analysis
    • Morozova O, Hirst M, Marra MA: Applications of new sequencing technologies for transcriptome analysis. Annual review of genomics and human genetics. 2009, 10: 135-151. 10.1146/annurev-genom-082908-145957.
    • (2009) Annual review of genomics and human genetics , vol.10 , pp. 135-151
    • Morozova, O.1    Hirst, M.2    Marra, M.A.3
  • 3
    • 57749195712 scopus 로고    scopus 로고
    • RNA-seq: a revolutionary tool for transcriptomics
    • Wang Z, Gerstein M, Snyder M: RNA-seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics. 2009, 10 (1): 57-63. 10.1038/nrg2484.
    • (2009) Nature Reviews Genetics , vol.10 , Issue.1 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 4
    • 77949481052 scopus 로고    scopus 로고
    • Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
    • Bullard J, Purdom E, Hansen K, Dudoit S: Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics. 2010, 11 (1): 94-10.1186/1471-2105-11-94.
    • (2010) BMC Bioinformatics , vol.11 , Issue.1 , pp. 94
    • Bullard, J.1    Purdom, E.2    Hansen, K.3    Dudoit, S.4
  • 5
    • 75249087100 scopus 로고    scopus 로고
    • edgeR: a bioconductor package for differential expression analysis of digital gene expression data
    • Robinson MD, McCarthy DJ, Smyth GK: edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010, 26 (1): 139-140. 10.1093/bioinformatics/btp616.
    • (2010) Bioinformatics , vol.26 , Issue.1 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 6
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders S, Huber W: Differential expression analysis for sequence count data. Genome Biol. 2010, 11 (10): 106-10.1186/gb-2010-11-10-r106.
    • (2010) Genome Biol , vol.11 , Issue.10 , pp. 106
    • Anders, S.1    Huber, W.2
  • 8
    • 84883067293 scopus 로고    scopus 로고
    • NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data
    • Bi Y, Davuluri RV: NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data. BMC bioinformatics. 2013, 14 (1): 262-10.1186/1471-2105-14-262.
    • (2013) BMC bioinformatics , vol.14 , Issue.1 , pp. 262
    • Bi, Y.1    Davuluri, R.V.2
  • 10
    • 84868017347 scopus 로고    scopus 로고
    • GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data
    • Feng J, Meyer CA, Wang Q, Liu JS, Liu XS, Zhang Y: GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data. Bioinformatics. 2012, 28 (21): 2782-2788. 10.1093/bioinformatics/bts515.
    • (2012) Bioinformatics , vol.28 , Issue.21 , pp. 2782-2788
    • Feng, J.1    Meyer, C.A.2    Wang, Q.3    Liu, J.S.4    Liu, X.S.5    Zhang, Y.6
  • 11
    • 0003991665 scopus 로고
    • An Introduction to the Bootstrap
    • Macmillan Publishers Limited
    • Efron B, Tibshirani R: An Introduction to the Bootstrap. 1993, Macmillan Publishers Limited
    • (1993)
    • Efron, B.1    Tibshirani, R.2
  • 12
    • 78049485688 scopus 로고    scopus 로고
    • Estimation of alternative splicing isoform frequencies from RNA-Seq data
    • Edited by: Moulton, V., Singh, M. Springer
    • Nicolae M, Mangul S, Mandoiu II, Zelikovsky A: Estimation of alternative splicing isoform frequencies from RNA-Seq data. Proc WABI Lecture Notes in Computer Science. Edited by: Moulton, V., Singh, M. 2010, Springer, ???, 6293: 202-214. 10.1007/978-3-642-15294-8_17.
    • (2010) Proc WABI Lecture Notes in Computer Science , vol.6293 , pp. 202-214
    • Nicolae, M.1    Mangul, S.2    Mandoiu, I.I.3    Zelikovsky, A.4
  • 13
    • 33748491517 scopus 로고    scopus 로고
    • The Microarray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements
    • MAQC Consortium: The Microarray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements. Nature Biotechnology. 2006, 24 (9): 1151-1161. 10.1038/nbt1239.
    • (2006) Nature Biotechnology , vol.24 , Issue.9 , pp. 1151-1161
  • 15
    • 84893242996 scopus 로고    scopus 로고
    • RNA-seq differential expression studies: more sequence or more replication?
    • Liu Y, Zhou J, White KP: RNA-seq differential expression studies: more sequence or more replication?. Bioinformatics. 2014, 30 (3): 301-304. 10.1093/bioinformatics/btt688.
    • (2014) Bioinformatics , vol.30 , Issue.3 , pp. 301-304
    • Liu, Y.1    Zhou, J.2    White, K.P.3
  • 17
    • 79961123152 scopus 로고    scopus 로고
    • RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
    • Bo Li CND: RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011, 12 (323):
    • (2011) BMC Bioinformatics , vol.12 , Issue.323
  • 18
    • 84969558444 scopus 로고    scopus 로고
    • External RNA Controls Consortium: Proposed methods for testing and selecting the ERCC external RNA controls
    • Reid LH: External RNA Controls Consortium: Proposed methods for testing and selecting the ERCC external RNA controls. BMC Genomics. 2005, 6 (150): 10.1186/1471-2164-6-1.
    • (2005) BMC Genomics , vol.6 , Issue.150
    • Reid, L.H.1
  • 19
    • 84969539966 scopus 로고
    • Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
    • Benjamini Y, Hochberg Y: Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society, Series B. 1995, 57 (1): 289-300.
    • (1995) Journal of the Royal Statistical Society, Series B , vol.57 , Issue.1 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 20
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg S: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology. 2009, 10 (3): 25-10.1186/gb-2009-10-3-r25.
    • (2009) Genome Biology , vol.10 , Issue.3 , pp. 25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.4
  • 21
    • 84897133117 scopus 로고    scopus 로고
    • MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping
    • Lee WP, Stromberg MP, Ward A, Stewart C, Garrison EP, Marth GT: MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping. PLoS ONE. 2014, 9 (3): 90581-10.1371/journal.pone.0090581.
    • (2014) PLoS ONE , vol.9 , Issue.3 , pp. 90581
    • Lee, W.P.1    Stromberg, M.P.2    Ward, A.3    Stewart, C.4    Garrison, E.P.5    Marth, G.T.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.