메뉴 건너뛰기




Volumn 18, Issue 2, 2008, Pages 709-729

A nonparametric empirical bayes approach to joint modeling of multiple sources of genomic data

Author keywords

ChIP chip; Computational biology; False discovery rate; Gene expression; Lrp; Microarray

Indexed keywords


EID: 47849132500     PISSN: 10170405     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (4)

References (44)
  • 1
    • 0034948896 scopus 로고    scopus 로고
    • A Bayesian framework for the analysis of microarray expression data: Regularized t-test and statistical inferences of gene changes
    • Baldi, P. and Long, A. D. (2001). A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 17, 509-519.
    • (2001) Bioinformatics , vol.17 , pp. 509-519
    • Baldi, P.1    Long, A.D.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. Roy. Statist. Soc. Ser. B 57, 289-300.
    • (1995) J. Roy. Statist. Soc. Ser. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 4
    • 31344436263 scopus 로고    scopus 로고
    • ChIPOTle: A use friendly tool for the analysis of ChIP-chip data
    • Buck, M. J., Nobel, A. B. and Lieb, J. D. (2005). ChIPOTle: a use friendly tool for the analysis of ChIP-chip data. Genome Biology 6:R97.
    • (2005) Genome Biology , vol.6
    • Buck, M.J.1    Nobel, A.B.2    Lieb, J.D.3
  • 5
    • 0037453009 scopus 로고    scopus 로고
    • Integrating regulatory motif discovery and genome-wide expression analysis
    • Conlon, E. M., Liu, X. S., Lieb, J. D. and Liu, J. S. (2003). Integrating regulatory motif discovery and genome-wide expression analysis. Proc. Natl. Acad. Sci. USA 100, 3339-3344.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 3339-3344
    • Conlon, E.M.1    Liu, X.S.2    Lieb, J.D.3    Liu, J.S.4
  • 6
    • 85044699856 scopus 로고    scopus 로고
    • Improved statistical tests for differential gene expression by shrinking variance components estimates
    • To appear in
    • Cui, X., Hwang, J. T. G., Qiu, J., Blades, N. J. and Churchill, C. R. (2004). Improved statistical tests for differential gene expression by shrinking variance components estimates. To appear in Biostatistics.
    • (2004) Biostatistics
    • Cui, X.1    Hwang, J.T.G.2    Qiu, J.3    Blades, N.J.4    Churchill, C.R.5
  • 7
    • 15844417905 scopus 로고    scopus 로고
    • A simple procedure for estimating the false discovery rate
    • Dalmasso, C., Broet, P. and Moreau, T. (2005). A simple procedure for estimating the false discovery rate. Bioinformatics 21, 660-668.
    • (2005) Bioinformatics , vol.21 , pp. 660-668
    • Dalmasso, C.1    Broet, P.2    Moreau, T.3
  • 8
    • 18444401138 scopus 로고    scopus 로고
    • A Bayesian mixture model for differential gene expression
    • Do, K.-A., Muller, P. and Tang, F. (2005). A Bayesian mixture model for differential gene expression. Appl. Statist. 54, 627-644.
    • (2005) Appl. Statist , vol.54 , pp. 627-644
    • Do, K.-A.1    Muller, P.2    Tang, F.3
  • 9
    • 2142732441 scopus 로고    scopus 로고
    • Large-scale simultaneous hypothesis testing: The choice of a null hypothesis
    • Efron, B. (2004). Large-scale simultaneous hypothesis testing: the choice of a null hypothesis. J. Amer. Statist. Assoc. 99, 96-104.
    • (2004) J. Amer. Statist. Assoc , vol.99 , pp. 96-104
    • Efron, B.1
  • 11
    • 0742306126 scopus 로고    scopus 로고
    • Enhanced software for model-based clustering, discriminant analysis, and density estimation: MCLUST
    • Fraley, C. and Raftery, A. E. (2003). Enhanced software for model-based clustering, discriminant analysis, and density estimation: MCLUST. J. Classification 20, 263-286.
    • (2003) J. Classification , vol.20 , pp. 263-286
    • Fraley, C.1    Raftery, A.E.2
  • 12
    • 2942582468 scopus 로고    scopus 로고
    • Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data
    • Gao, F., Foat, B. C. and Bussemaker, H. J. (2004). Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC Bioinformatics 5:31.
    • (2004) BMC Bioinformatics , vol.5 , pp. 31
    • Gao, F.1    Foat, B.C.2    Bussemaker, H.J.3
  • 13
    • 0034564606 scopus 로고    scopus 로고
    • Finding regulatory elements using joint likelihoods for sequence and expression profile data
    • Holmes, I. and Bruno, W. J. (2000). Finding regulatory elements using joint likelihoods for sequence and expression profile data. Proc. Int. Conf. Intell. Syst. Mol. Biol. 8, 202-210.
    • (2000) Proc. Int. Conf. Intell. Syst. Mol. Biol , vol.8 , pp. 202-210
    • Holmes, I.1    Bruno, W.J.2
  • 14
    • 0030305457 scopus 로고    scopus 로고
    • R: A language for data analysis and graphics
    • Ihaka, R. and Gentleman, R. (1996). R: A language for data analysis and graphics. J. Comput. Graph. Statist. 5, 299-314.
    • (1996) J. Comput. Graph. Statist , vol.5 , pp. 299-314
    • Ihaka, R.1    Gentleman, R.2
  • 15
    • 24644462724 scopus 로고    scopus 로고
    • TileMap: Create chromosomal map of tiling array hybridizations
    • Ji, H. and Wong, W. H. (2005). TileMap: create chromosomal map of tiling array hybridizations. Bioinformatics 21, 3629-3636.
    • (2005) Bioinformatics , vol.21 , pp. 3629-3636
    • Ji, H.1    Wong, W.H.2
  • 16
    • 0346888587 scopus 로고    scopus 로고
    • On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles
    • Kendziorski, C. M., Newton, M. A., Lan, H. and Gould, M. N. (2003). On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles. Statist. Medicine 22, 3899-3914.
    • (2003) Statist. Medicine , vol.22 , pp. 3899-3914
    • Kendziorski, C.M.1    Newton, M.A.2    Lan, H.3    Gould, M.N.4
  • 17
    • 0036966431 scopus 로고    scopus 로고
    • A statistical model for investigating binding probabilities of DNA nucleotide sequences using microarrays
    • Lee, M.-L. T., Bulyk, M. L., Whitmore, G. A. and Church, G. M. (2002). A statistical model for investigating binding probabilities of DNA nucleotide sequences using microarrays. Biometrics 58, 981-988.
    • (2002) Biometrics , vol.58 , pp. 981-988
    • Lee, M.-L.T.1    Bulyk, M.L.2    Whitmore, G.A.3    Church, G.M.4
  • 19
    • 0442325057 scopus 로고    scopus 로고
    • Markovian structures in biological sequence alignments
    • Liu, J. S., Neuwald, A. F. and Lawrence, C. E. (1999). Markovian structures in biological sequence alignments. J. Amer. Statist. Assoc. 94, 1-15.
    • (1999) J. Amer. Statist. Assoc , vol.94 , pp. 1-15
    • Liu, J.S.1    Neuwald, A.F.2    Lawrence, C.E.3
  • 20
    • 0036324753 scopus 로고    scopus 로고
    • An algorithm for finding protein-DNA binding sites with applications to chromatin- immunoprecipitation microarray experiments
    • Liu, X. S., Brutlag, D. L. and Liu, J. S. (2002). An algorithm for finding protein-DNA binding sites with applications to chromatin- immunoprecipitation microarray experiments. Nat. Biotechnol. 20, 835-839.
    • (2002) Nat. Biotechnol , vol.20 , pp. 835-839
    • Liu, X.S.1    Brutlag, D.L.2    Liu, J.S.3
  • 21
    • 33745606461 scopus 로고    scopus 로고
    • A simple implementation of a normal mixture approach to differential gene expression in multiclass microarrays
    • McLachlan, G.J., Bean, R.W., Jones, L.B.-T. (2006). A simple implementation of a normal mixture approach to differential gene expression in multiclass microarrays. Bioinformatics 22, 1608-1615.
    • (2006) Bioinformatics , vol.22 , pp. 1608-1615
    • McLachlan, G.J.1    Bean, R.W.2    Jones, L.B.-T.3
  • 22
    • 0034923013 scopus 로고    scopus 로고
    • Newton, M. A, Kendziorski, C. M., Richmond, C. C., Blattner, F.R. and Tsui, K. W. (2001). On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data. J. Computational Biology 8, 37-52.
    • Newton, M. A, Kendziorski, C. M., Richmond, C. C., Blattner, F.R. and Tsui, K. W. (2001). On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data. J. Computational Biology 8, 37-52.
  • 23
    • 4444235995 scopus 로고    scopus 로고
    • Detecting differential gene expression with a semiparametric hierarchical mixture method
    • Newton, M. A., Noueiry, A., Sarkar, D. and Ahlquist, P. (2004). Detecting differential gene expression with a semiparametric hierarchical mixture method. Biostatistics 5, 155-176.
    • (2004) Biostatistics , vol.5 , pp. 155-176
    • Newton, M.A.1    Noueiry, A.2    Sarkar, D.3    Ahlquist, P.4
  • 24
    • 0028977927 scopus 로고
    • Regulation of lrp gene expression by H-NS and Lrp proteins in Escherichia coli: Dominant negative mutations in lrp
    • Oshima, T., Ito, K., Kabayama, H. and Nakamura, Y. (1995). Regulation of lrp gene expression by H-NS and Lrp proteins in Escherichia coli: dominant negative mutations in lrp. Mol Gen Genet. 247, 521-528.
    • (1995) Mol Gen Genet , vol.247 , pp. 521-528
    • Oshima, T.1    Ito, K.2    Kabayama, H.3    Nakamura, Y.4
  • 25
    • 0035999977 scopus 로고    scopus 로고
    • A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments
    • Pan, W. (2002). A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments. Bioinformatics 12, 546-554.
    • (2002) Bioinformatics , vol.12 , pp. 546-554
    • Pan, W.1
  • 26
    • 0041592555 scopus 로고    scopus 로고
    • On the use of permutation in and the performance of a class of nonparametric methods to detect differential gene expression
    • Pan, W. (2003). On the use of permutation in and the performance of a class of nonparametric methods to detect differential gene expression. Bioinformatics 19, 1333-1340.
    • (2003) Bioinformatics , vol.19 , pp. 1333-1340
    • Pan, W.1
  • 27
    • 2142854576 scopus 로고    scopus 로고
    • A mixture model approach to detecting differentially expressed genes with microarray data
    • Pan, W., Lin, J. and Le, C. (2003). A mixture model approach to detecting differentially expressed genes with microarray data. Functional and Integrative Genomics 3, 117-124.
    • (2003) Functional and Integrative Genomics , vol.3 , pp. 117-124
    • Pan, W.1    Lin, J.2    Le, C.3
  • 28
    • 4444294164 scopus 로고    scopus 로고
    • Improving false discovery rate estimation
    • Pounds, S. and Cheng, C. (2004). Improving false discovery rate estimation. Bioinformatics, 20, 1737-1745.
    • (2004) Bioinformatics , vol.20 , pp. 1737-1745
    • Pounds, S.1    Cheng, C.2
  • 30
    • 0038048164 scopus 로고    scopus 로고
    • Statistical issues in cDNA microarray data analysis
    • Edited by M. J. Brownstein and A. B. Khodursky, Methods in Molecular Biology 224, Humana Press, Totowa, NJ
    • Smyth, G. K., Yang, Y. H. and Speed, T. (2003). Statistical issues in cDNA microarray data analysis. In Functional Genomics: Methods and Protocols (Edited by M. J. Brownstein and A. B. Khodursky), 111-136, Methods in Molecular Biology Volume 224, Humana Press, Totowa, NJ.
    • (2003) Functional Genomics: Methods and Protocols , pp. 111-136
    • Smyth, G.K.1    Yang, Y.H.2    Speed, T.3
  • 31
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genome-wide experiments
    • Storey, J. D. and Tibshirani, R. (2003). Statistical significance for genome-wide experiments. Proc. Natl Acad. Sci. USA 100, 9440-9445.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2
  • 32
    • 33744501241 scopus 로고    scopus 로고
    • Bayesian error analysis model for reconstructing transcriptional regulatory networks
    • Sun, N., Carroll, R.J. and Zhao, H. (2006). Bayesian error analysis model for reconstructing transcriptional regulatory networks. Proc. Natl. Acad. Sci. USA 103, 7988-7993.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 7988-7993
    • Sun, N.1    Carroll, R.J.2    Zhao, H.3
  • 33
    • 0037109068 scopus 로고    scopus 로고
    • Adaptation to famine: A family of stationary-phase genes revealed by microarray analysis
    • Tani, T., Khodursky, A., Blumenthal, R., Brown, P., and Matthews, R. (2002). Adaptation to famine: A family of stationary-phase genes revealed by microarray analysis. Proc. Natl. Acad. Sci. USA 99, 13471-13476.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 13471-13476
    • Tani, T.1    Khodursky, A.2    Blumenthal, R.3    Brown, P.4    Matthews, R.5
  • 34
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • Tusher, V.G., Tibshirani, R. and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. Proc. Nat. Acad. Sci. USA 98, 5116-5121.
    • (2001) Proc. Nat. Acad. Sci. USA , vol.98 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 35
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S. G., Fields, S., Bork, P. (2002). Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417, 399-403.
    • (2002) Nature , vol.417 , pp. 399-403
    • von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6    Bork, P.7
  • 37
    • 13844319583 scopus 로고    scopus 로고
    • Inference of combinatorial regulation in yeast transcriptional networks: A case study of sporulation
    • Wang, W., Cherry, J. M., Nochomovitz, Y., Jolly, E., Botstein, D. and Li, H. (2005). Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation. Proc. Nat. Acad. Sci. USA 102, 1998-2003.
    • (2005) Proc. Nat. Acad. Sci. USA , vol.102 , pp. 1998-2003
    • Wang, W.1    Cherry, J.M.2    Nochomovitz, Y.3    Jolly, E.4    Botstein, D.5    Li, H.6
  • 38
    • 0348143180 scopus 로고    scopus 로고
    • A random variance model for detection of differential gene expression in small microarray experiments
    • Wright, G. W. and Simon, R. M. (2003). A random variance model for detection of differential gene expression in small microarray experiments. Bioinformatics 19, 2448-2455.
    • (2003) Bioinformatics , vol.19 , pp. 2448-2455
    • Wright, G.W.1    Simon, R.M.2
  • 39
    • 31044452892 scopus 로고    scopus 로고
    • Gene function prediction by a combined analysis of gene expression data and protein-protein interaction data
    • Xiao, G. and Pan, W. (2005). Gene function prediction by a combined analysis of gene expression data and protein-protein interaction data. J. Bioinformatics and Computational Biology 3, 1371-1389.
    • (2005) J. Bioinformatics and Computational Biology , vol.3 , pp. 1371-1389
    • Xiao, G.1    Pan, W.2
  • 40
  • 41
    • 34247590196 scopus 로고    scopus 로고
    • Incorporating prior information via shrinkage: A combined analysis of genome-wide location data and gene expression data
    • Xie, Y., Pan, W., Jeong, K. S. and Khodursky, A. (2007). Incorporating prior information via shrinkage: a combined analysis of genome-wide location data and gene expression data. Statist. Medicine 26, 2258-2275.
    • (2007) Statist. Medicine , vol.26 , pp. 2258-2275
    • Xie, Y.1    Pan, W.2    Jeong, K.S.3    Khodursky, A.4
  • 42
    • 0037101842 scopus 로고    scopus 로고
    • A regression-based method to identify differentially expressed genes in microarray time course studies and its application in an inducible Huntington's disease transgenic model
    • Xu, X. L., Olson, J. M. and Zhao, L. P. (2002). A regression-based method to identify differentially expressed genes in microarray time course studies and its application in an inducible Huntington's disease transgenic model. Human Molecular Genetics 11, 1977-1985.
    • (2002) Human Molecular Genetics , vol.11 , pp. 1977-1985
    • Xu, X.L.1    Olson, J.M.2    Zhao, L.P.3
  • 44
    • 21844466280 scopus 로고    scopus 로고
    • DNA-protein binding and gene expression patterns
    • Science and Statistics: A Festschrift for Terry Speed Edited by D. R. Goldstein
    • Zhao, H., Wu, B. and Sun, N. (2003). DNA-protein binding and gene expression patterns. In Science and Statistics: A Festschrift for Terry Speed (Edited by D. R. Goldstein), 259-274. IMS Lecture Notes-Monograph Series 40.
    • (2003) IMS Lecture Notes-Monograph Series , vol.40 , pp. 259-274
    • Zhao, H.1    Wu, B.2    Sun, N.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.