메뉴 건너뛰기




Volumn 11, Issue , 2010, Pages

BaySeq: Empirical Bayesian methods for identifying differential expression in sequence count data

Author keywords

[No Author keywords available]

Indexed keywords

ANALYSIS OF DATA; DIFFERENTIAL EXPRESSIONS; EMPIRICAL BAYES APPROACH; EMPIRICAL BAYESIAN METHOD; EXPRESSION LEVELS; HIGH-THROUGHPUT SEQUENCING; NEGATIVE BINOMIAL DISTRIBUTION; PRIOR DISTRIBUTION;

EID: 77955298482     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-422     Document Type: Article
Times cited : (586)

References (25)
  • 2
    • 33750953227 scopus 로고    scopus 로고
    • Whole-genome re-sequencing
    • 10.1016/j.gde.2006.10.009, 17055251
    • Bentley DR. Whole-genome re-sequencing. Curr Opin Genet Dev 2006, 16:545-552. 10.1016/j.gde.2006.10.009, 17055251.
    • (2006) Curr Opin Genet Dev , vol.16 , pp. 545-552
    • Bentley, D.R.1
  • 3
    • 37749031255 scopus 로고    scopus 로고
    • Next-generation sequencing transforms today's biology
    • 10.1038/nmeth1156, 18165802
    • Schuster SC. Next-generation sequencing transforms today's biology. Nat Methods 2008, 5:16-18. 10.1038/nmeth1156, 18165802.
    • (2008) Nat Methods , vol.5 , pp. 16-18
    • Schuster, S.C.1
  • 4
    • 39649117755 scopus 로고    scopus 로고
    • The impact of next-generation sequencing technology on genetics
    • Mardis ER. The impact of next-generation sequencing technology on genetics. Trends Genet 2008, 24:133-141.
    • (2008) Trends Genet , vol.24 , pp. 133-141
    • Mardis, E.R.1
  • 5
    • 0028789793 scopus 로고
    • Serial analysis of gene expression
    • 10.1126/science.270.5235.484, 7570003
    • Velculescu VE, Zhang L, Vogelstein B, Kinzler KW. Serial analysis of gene expression. Science 1995, 270:484-487. 10.1126/science.270.5235.484, 7570003.
    • (1995) Science , vol.270 , pp. 484-487
    • Velculescu, V.E.1    Zhang, L.2    Vogelstein, B.3    Kinzler, K.W.4
  • 6
    • 13244298225 scopus 로고    scopus 로고
    • Overdispersed logistic regression for SAGE: modelling multiple groups and covariates
    • 10.1186/1471-2105-5-144, 524524, 15469612
    • Baggerly KA, Deng L, Morris JS, Aldaz CM. Overdispersed logistic regression for SAGE: modelling multiple groups and covariates. BMC Bioinformatics 2004, 5:144. 10.1186/1471-2105-5-144, 524524, 15469612.
    • (2004) BMC Bioinformatics , vol.5 , pp. 144
    • Baggerly, K.A.1    Deng, L.2    Morris, J.S.3    Aldaz, C.M.4
  • 7
    • 25444469952 scopus 로고    scopus 로고
    • Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach
    • 10.1186/1471-2105-6-165, 1189357, 15987513
    • Lu J, Tomfohr JK, Kepler TB. Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach. BMC Bioinformatics 2005, 6:165. 10.1186/1471-2105-6-165, 1189357, 15987513.
    • (2005) BMC Bioinformatics , vol.6 , pp. 165
    • Lu, J.1    Tomfohr, J.K.2    Kepler, T.B.3
  • 8
    • 41149085992 scopus 로고    scopus 로고
    • Small-sample estimation of negative binomial dispersion, with applications to SAGE data
    • 10.1093/biostatistics/kxm030, 17728317
    • Robinson MD, Smyth GK. Small-sample estimation of negative binomial dispersion, with applications to SAGE data. Biostatistics 2008, 9:321-332. 10.1093/biostatistics/kxm030, 17728317.
    • (2008) Biostatistics , vol.9 , pp. 321-332
    • Robinson, M.D.1    Smyth, G.K.2
  • 9
    • 36448981743 scopus 로고    scopus 로고
    • Moderated statistical tests for assessing differences in tag abundance
    • 10.1093/bioinformatics/btm453, 17881408
    • Robinson MD, Smyth GK. Moderated statistical tests for assessing differences in tag abundance. Bioinformatics 2007, 23:2881-2887. 10.1093/bioinformatics/btm453, 17881408.
    • (2007) Bioinformatics , vol.23 , pp. 2881-2887
    • Robinson, M.D.1    Smyth, G.K.2
  • 10
    • 75249095274 scopus 로고    scopus 로고
    • DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
    • 10.1093/bioinformatics/btp612, 19855105
    • Wang L, Feng Z, Wang X, Wang X, Zhang X. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 2010, 26:136-138. 10.1093/bioinformatics/btp612, 19855105.
    • (2010) Bioinformatics , vol.26 , pp. 136-138
    • Wang, L.1    Feng, Z.2    Wang, X.3    Wang, X.4    Zhang, X.5
  • 11
    • 84866622527 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders S, Huber W. Differential expression analysis for sequence count data. Nature Precedings 2010, , http://precedings.nature.com/documents/4282/version/2
    • (2010) Nature Precedings
    • Anders, S.1    Huber, W.2
  • 12
    • 77949481052 scopus 로고    scopus 로고
    • Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
    • 10.1186/1471-2105-11-94, 2838869, 20167110
    • Bullard JH, Purdom E, Hansen KD, Dudoit S. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 2010, 11:94. 10.1186/1471-2105-11-94, 2838869, 20167110.
    • (2010) BMC Bioinformatics , vol.11 , pp. 94
    • Bullard, J.H.1    Purdom, E.2    Hansen, K.D.3    Dudoit, S.4
  • 13
    • 84972543992 scopus 로고
    • Methods for Approximating Integrals in Statistics with Special Emphasis on Bayesian Integration Problems
    • Evans M, Swartz T. Methods for Approximating Integrals in Statistics with Special Emphasis on Bayesian Integration Problems. Statistical Science 1995, 10(3):254-272.
    • (1995) Statistical Science , vol.10 , Issue.3 , pp. 254-272
    • Evans, M.1    Swartz, T.2
  • 14
    • 33749995538 scopus 로고    scopus 로고
    • Quasi-likelihood and psuedo-likelihood are not the same thing
    • Nelder J. Quasi-likelihood and psuedo-likelihood are not the same thing. Journal of Applied Statistics 2000, 27(8):1007-1011.
    • (2000) Journal of Applied Statistics , vol.27 , Issue.8 , pp. 1007-1011
    • Nelder, J.1
  • 15
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
    • 10.2202/1544-6115.1027, 16646809
    • Smyth GK. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 2004, 3. 10.2202/1544-6115.1027, 16646809.
    • (2004) Statistical Applications in Genetics and Molecular Biology , vol.3
    • Smyth, G.K.1
  • 17
    • 77956172395 scopus 로고    scopus 로고
    • EdgeR: Methods for differential expression in digital gene expression datasets
    • Robinson M. edgeR: Methods for differential expression in digital gene expression datasets. Bioconductor 2009,
    • (2009) Bioconductor
    • Robinson, M.1
  • 18
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: a Bioconductor package for differential expression analysis of digital gene expression data
    • 10.1093/bioinformatics/btp616, 2796818, 19910308
    • Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26:139-140. 10.1093/bioinformatics/btp616, 2796818, 19910308.
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 21
    • 4644286235 scopus 로고    scopus 로고
    • SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis
    • 10.1101/gad.1231804, 522987, 15466488
    • Peragine A, Yoshikawa M, Wu G, Albrecht HL, Poethig RS. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev 2004, 18:2368-2379. 10.1101/gad.1231804, 522987, 15466488.
    • (2004) Genes Dev , vol.18 , pp. 2368-2379
    • Peragine, A.1    Yoshikawa, M.2    Wu, G.3    Albrecht, H.L.4    Poethig, R.S.5
  • 23
    • 46249132980 scopus 로고    scopus 로고
    • PatMaN: rapid alignment of short sequences to large databases
    • 10.1093/bioinformatics/btn223, 2718670, 18467344
    • Prüfer K, Stenzel U, Dannemann M, Green RE, Lachmann M, Kelso J. PatMaN: rapid alignment of short sequences to large databases. Bioinformatics 2008, 24:1530-1531. 10.1093/bioinformatics/btn223, 2718670, 18467344.
    • (2008) Bioinformatics , vol.24 , pp. 1530-1531
    • Prüfer, K.1    Stenzel, U.2    Dannemann, M.3    Green, R.E.4    Lachmann, M.5    Kelso, J.6
  • 25
    • 35748932852 scopus 로고    scopus 로고
    • R Foundation for Statistical Computing, Vienna, Austria, [ISBN 3-900051-07-0], R Development Core Team
    • R Development Core Team R: A Language and Environment for Statistical Computing 2007, R Foundation for Statistical Computing, Vienna, Austria, [ISBN 3-900051-07-0], R Development Core Team., http://www.R-project.org
    • (2007) R: A Language and Environment for Statistical Computing


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.