메뉴 건너뛰기




Volumn 31, Issue 16, 2015, Pages 2614-2622

EBSeq-HMM: A Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments

Author keywords

[No Author keywords available]

Indexed keywords

BAYES THEOREM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HIGH THROUGHPUT SEQUENCING; HUMAN; PROCEDURES; SEQUENCE ANALYSIS; SOFTWARE;

EID: 84939501639     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv193     Document Type: Article
Times cited : (75)

References (33)
  • 1
    • 84855191706 scopus 로고    scopus 로고
    • Markov-switching autoregressive models for wind time series
    • Ailliot, P. and Monbet, V. (2012) Markov-switching autoregressive models for wind time series. Environ. Model. Softw. , 30, 92-101.
    • (2012) Environ. Model. Softw. , vol.30 , pp. 92-101
    • Ailliot, P.1    Monbet, V.2
  • 2
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol. , 11, R106.
    • (2010) Genome Biol. , vol.11 , pp. R106
    • Anders, S.1    Huber, W.2
  • 3
    • 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. Stat. Soc. Ser. B (Methodological) , 57, 289-300.
    • (1995) J. R. Stat. Soc. Ser. B (Methodological) , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 5
    • 77949481052 scopus 로고    scopus 로고
    • Evaluation of statistical methods for normalization and differential expression in mRNA-seq experiments
    • Bullard, J. H. et al. (2010) Evaluation of statistical methods for normalization and differential expression in mRNA-seq experiments. BMC Bioinformatics, 11, 94.
    • (2010) BMC Bioinformatics , vol.11 , pp. 94
    • Bullard, J.H.1
  • 6
    • 70849106865 scopus 로고    scopus 로고
    • Anatomic demarcation of cells: Genes to patterns
    • Chang, H. (2009) Anatomic demarcation of cells: genes to patterns. Science, 326, 1206-1207.
    • (2009) Science , vol.326 , pp. 1206-1207
    • Chang, H.1
  • 7
    • 33646147811 scopus 로고    scopus 로고
    • MaSigPro: A method to identify significantly differential expression profiles in time-course microarray experiments
    • Conesa, A. et al. (2006) maSigPro: A method to identify significantly differential expression profiles in time-course microarray experiments. Bioinformatics, 22, 1096-1102.
    • (2006) Bioinformatics , vol.22 , pp. 1096-1102
    • Conesa, A.1
  • 8
    • 84855989774 scopus 로고    scopus 로고
    • Fast computation and applications of genome mappability
    • Derrien, T. et al. (2012) Fast computation and applications of genome mappability. PLoS One, 7, e30377.
    • (2012) PLoS One , vol.7 , pp. e30377
    • Derrien, T.1
  • 9
    • 28644452470 scopus 로고    scopus 로고
    • Clustering short time series gene expression data
    • Ernst, J. et al. (2005) Clustering short time series gene expression data. Bioinformatics, 21(Suppl. 1) , i159-i168.
    • (2005) Bioinformatics , vol.21 , pp. i159-i168
    • Ernst, J.1
  • 10
    • 0036100833 scopus 로고    scopus 로고
    • Analysis techniques for microarray time-series data
    • Filkov, V. et al. (2002) Analysis techniques for microarray time-series data. J. Comput. Biol. , 9, 317-330.
    • (2002) J. Comput. Biol. , vol.9 , pp. 317-330
    • Filkov, V.1
  • 11
    • 84863992953 scopus 로고    scopus 로고
    • Identifying differentially expressed transcripts from RNA-seq data with biological variation
    • Glaus, P. et al. (2012) Identifying differentially expressed transcripts from RNA-seq data with biological variation. Bioinformatics, 28, 1721-1728.
    • (2012) Bioinformatics , vol.28 , pp. 1721-1728
    • Glaus, P.1
  • 12
    • 0001342006 scopus 로고
    • A new approach to the economic analysis of nonstationary time series and the business cycle
    • Hamilton, J. D. (1989) A new approach to the economic analysis of nonstationary time series and the business cycle. Econometrica, 357-384.
    • (1989) Econometrica , pp. 357-384
    • Hamilton, J.D.1
  • 13
    • 77955298482 scopus 로고    scopus 로고
    • BaySeq: Empirical Bayesian methods for identifying differential expression in sequence count data
    • Hardcastle, T. J. and Kelly, K. A. (2010) baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics, 11, 422.
    • (2010) BMC Bioinformatics , vol.11 , pp. 422
    • Hardcastle, T.J.1    Kelly, K.A.2
  • 14
    • 78651447845 scopus 로고    scopus 로고
    • The uniqueome: A mappability resource for short-tag sequencing
    • Koehler, R. et al. (2011) The uniqueome: A mappability resource for short-tag sequencing. Bioinformatics, 27, 272-274.
    • (2011) Bioinformatics , vol.27 , pp. 272-274
    • Koehler, R.1
  • 15
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B. et al. (2010) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. , 10, R25.
    • (2010) Genome Biol. , vol.10 , pp. R25
    • Langmead, B.1
  • 16
    • 84896735766 scopus 로고    scopus 로고
    • Voom: Precision weights unlock linear model analysis tools for RNA-seq read counts
    • Law, C. W. et al. (2014) Voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. , 15, R29.
    • (2014) Genome Biol. , vol.15 , pp. R29
    • Law, C.W.1
  • 17
    • 84876263777 scopus 로고    scopus 로고
    • EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments
    • Leng, N. et al. (2013) EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics, 29, 1035-1043.
    • (2013) Bioinformatics , vol.29 , pp. 1035-1043
    • Leng, N.1
  • 18
    • 79961123152 scopus 로고    scopus 로고
    • RSEM: Accurate transcript quantification from RNA-seq data with or without a reference genome
    • Li, B. and Dewey, C. N. (2011) RSEM: Accurate transcript quantification from RNA-seq data with or without a reference genome. BMC Bioinformatics, 12, 323.
    • (2011) BMC Bioinformatics , vol.12 , pp. 323
    • Li, B.1    Dewey, C.N.2
  • 19
    • 84924629414 scopus 로고    scopus 로고
    • Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
    • Love, M. I. et al. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. , 15, 550.
    • (2014) Genome Biol. , vol.15 , pp. 550
    • Love, M.I.1
  • 20
    • 0037339264 scopus 로고    scopus 로고
    • Clustering of time-course gene expression data using a mixed-effects model with b-splines
    • Luan, Y. and Li, H. (2003) Clustering of time-course gene expression data using a mixed-effects model with b-splines. Bioinformatics, 19, 474-482.
    • (2003) Bioinformatics , vol.19 , pp. 474-482
    • Luan, Y.1    Li, H.2
  • 21
    • 78649959694 scopus 로고    scopus 로고
    • Identifying differentially expressed genes in time course microarray data
    • Ma, P. et al. (2009) Identifying differentially expressed genes in time course microarray data. Stat. Biosciences, 1, 144-159.
    • (2009) Stat. Biosciences , vol.1 , pp. 144-159
    • Ma, P.1
  • 22
    • 84907546454 scopus 로고    scopus 로고
    • Next maSigPro: Updating maSigPro bioconductor package for RNA-seq time series
    • Nueda, M. J. et al. (2014) Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series. Bioinformatics. , 30, 2598-2602.
    • (2014) Bioinformatics. , vol.30 , pp. 2598-2602
    • Nueda, M.J.1
  • 23
    • 33746658155 scopus 로고    scopus 로고
    • Anatomic demarcation by positional variation in fibroblast gene expression programs
    • Rinn, J. et al. (2006) Anatomic demarcation by positional variation in fibroblast gene expression programs. PLoS Genet. , 2, e119.
    • (2006) PLoS Genet. , vol.2 , pp. e119
    • Rinn, J.1
  • 24
    • 77953176036 scopus 로고    scopus 로고
    • A scaling normalization method for differential expression analysis of RNA-seq data
    • Robinson, M. D. and Oshlack, A. (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. , 11, R25.
    • (2010) Genome Biol. , vol.11 , pp. R25
    • Robinson, M.D.1    Oshlack, A.2
  • 25
    • 36448981743 scopus 로고    scopus 로고
    • Moderated statistical tests for assessing differences in tag abundance
    • Robinson, M. D. and Smyth, G. K. (2007) Moderated statistical tests for assessing differences in tag abundance. Bioinformatics, 23, 2881-2887.
    • (2007) Bioinformatics , vol.23 , pp. 2881-2887
    • Robinson, M.D.1    Smyth, G.K.2
  • 26
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: A bioconductor package for differential expression analysis of digital gene expression data
    • Robinson, M. D. et al. (2010) edgeR: A bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26, 139-140.
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1
  • 27
    • 33745211903 scopus 로고    scopus 로고
    • Bayes risk minimization using metric loss functions
    • Schlüter, R. et al. (2005) Bayes risk minimization using metric loss functions. In: INTERSPEECH, pp. 1449-1452.
    • (2005) INTERSPEECH , pp. 1449-1452
    • Schlüter, R.1
  • 28
    • 84894213042 scopus 로고    scopus 로고
    • RSeqDiff: Detecting differential isoform expression from RNA-seq data using hierarchical likelihood ratio test
    • Shi, Y. and Jiang, H. (2013) rSeqDiff: detecting differential isoform expression from RNA-seq data using hierarchical likelihood ratio test. PLoS One, 8, e79448.
    • (2013) PLoS One , vol.8 , pp. e79448
    • Shi, Y.1    Jiang, H.2
  • 29
    • 85023639437 scopus 로고    scopus 로고
    • On the negative binomial approximation to the beta-negative binomial distribution
    • Teerapabolarn, K. (2008) On the negative binomial approximation to the beta-negative binomial distribution. Int. J. Contemp. Math. Sci. , 3, 1213-1216.
    • (2008) Int. J. Contemp. Math. Sci. , vol.3 , pp. 1213-1216
    • Teerapabolarn, K.1
  • 30
    • 84872198346 scopus 로고    scopus 로고
    • Differential analysis of gene regulation at transcript resolution with RNA-seq
    • Trapnell, C. et al. (2012) Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat. Biotechnol. , 31, 46-53.
    • (2012) Nat. Biotechnol. , vol.31 , pp. 46-53
    • Trapnell, C.1
  • 31
    • 66349106449 scopus 로고    scopus 로고
    • Regeneration, repair and remembering identity: The three Rs of Hox gene expression
    • Wang, K. et al. (2009) Regeneration, repair and remembering identity: The three Rs of Hox gene expression. Trends Cell Biol. , 19, 268-275.
    • (2009) Trends Cell Biol. , vol.19 , pp. 268-275
    • Wang, K.1
  • 32
    • 33846036999 scopus 로고    scopus 로고
    • Hidden Markov models for microarray time course data in multiple biological conditions
    • Yuan, M. and Kendziorski, C. (2006) Hidden Markov models for microarray time course data in multiple biological conditions. J. Am. Stat. Assoc. , 101, 1323-1332.
    • (2006) J. Am. Stat. Assoc. , vol.101 , pp. 1323-1332
    • Yuan, M.1    Kendziorski, C.2
  • 33
    • 34547816223 scopus 로고    scopus 로고
    • The role of Hox genes during vertebrate limb development
    • Zakany, J. and Duboule, D. (2007) The role of Hox genes during vertebrate limb development. Curr. Opin. Genet. Dev. , 17, 359-366.
    • (2007) Curr. Opin. Genet. Dev. , vol.17 , pp. 359-366
    • Zakany, J.1    Duboule, D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.