메뉴 건너뛰기




Volumn 7, Issue , 2006, Pages

Bayesian models for pooling microarray studies with multiple sources of replications

Author keywords

[No Author keywords available]

Indexed keywords

BACILLUS SUBTILIS; BAYESIAN ESTIMATE; BAYESIAN HIERARCHICAL MODEL; DIFFERENTIAL EXPRESSIONS; DIFFERENTIALLY EXPRESSED GENE; FALSE DISCOVERY RATE; POSTERIOR PROBABILITY; SIMULATION STUDIES;

EID: 33747017793     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-247     Document Type: Article
Times cited : (42)

References (44)
  • 1
    • 0034948896 scopus 로고    scopus 로고
    • Bayesian framework for the analysis of microarray expression data: Reguralized t-test and statistical inferences of gene changes
    • Baldi P, Long AD: Bayesian framework for the analysis of microarray expression data: reguralized t-test and statistical inferences of gene changes. Bioinformatics 2001, 17:509-519.
    • (2001) Bioinformatics , vol.17 , pp. 509-519
    • Baldi, P.1    Long, A.D.2
  • 2
    • 0035875553 scopus 로고    scopus 로고
    • Issues in cDNA microarray analysis: Quality filtering, channel normalization, models of variations and assessment of gene effects
    • Tseng GC, Oh MK, Rohlin L, Liao JC, Wong WH: Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res 2001, 29:2549-2557.
    • (2001) Nucleic Acids Res , vol.29 , pp. 2549-2557
    • Tseng, G.C.1    Oh, M.K.2    Rohlin, L.3    Liao, J.C.4    Wong, W.H.5
  • 3
    • 0037975700 scopus 로고    scopus 로고
    • Bayesian analysis of gene expression levels: Statistical quantification of relative mRNA level across multiple treatments or samples
    • research0071.1-71.16
    • Townsend JP, Hartl DL: Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple treatments or samples. Genome Biology 2002, 3:research0071.1-71.16.
    • (2002) Genome Biology , vol.3
    • Townsend, J.P.1    Hartl, D.L.2
  • 5
    • 0034923013 scopus 로고    scopus 로고
    • On Differential Variability of Expression Ratios: Improving Statistical Inference About Gene Expression Changes From Microarray Data
    • Newton MA, Kendziorski CM, Richmond CS, Blattner FR, Tsui KW: On Differential Variability of Expression Ratios: Improving Statistical Inference About Gene Expression Changes From Microarray Data. Journal of Computational Biology 2001, 8:37-52.
    • (2001) Journal of Computational Biology , vol.8 , pp. 37-52
    • Newton, M.A.1    Kendziorski, C.M.2    Richmond, C.S.3    Blattner, F.R.4    Tsui, K.W.5
  • 7
    • 0036401627 scopus 로고    scopus 로고
    • Bayesian hierarchical model for identifying changes in gene expression from microarray experiments
    • Broët P, Richardson S, Radvanyi F: Bayesian hierarchical model for identifying changes in gene expression from microarray experiments. Journal of Computational Biology 2002, 9:671-683.
    • (2002) Journal of Computational Biology , vol.9 , pp. 671-683
    • Broët, P.1    Richardson, S.2    Radvanyi, F.3
  • 10
    • 0035999977 scopus 로고    scopus 로고
    • A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments
    • Pan W: A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments. Bioinformatics 2002, 18:546-554.
    • (2002) Bioinformatics , vol.18 , pp. 546-554
    • Pan, W.1
  • 11
    • 0346888587 scopus 로고    scopus 로고
    • On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles
    • Kendziorski CM, Newton MA, Lan H, Gould MN: On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles. Statistics in Medicine 2003, 22:3899-3914.
    • (2003) Statistics in Medicine , vol.22 , pp. 3899-3914
    • Kendziorski, C.M.1    Newton, M.A.2    Lan, H.3    Gould, M.N.4
  • 12
    • 4444235995 scopus 로고    scopus 로고
    • Detecting differential gene expression with a semiparametric hierarchical mixture method
    • Newton MA, Noueiry A, Sarkar D, Ahlquist P: Detecting differential gene expression with a semiparametric hierarchical mixture method. Biostatistics 2004, 5:155-176.
    • (2004) Biostatistics , vol.5 , pp. 155-176
    • Newton, M.A.1    Noueiry, A.2    Sarkar, D.3    Ahlquist, P.4
  • 14
    • 0042744696 scopus 로고    scopus 로고
    • Detecting Differentially Expressed Genes in Microarrays Using Bayesian Model Selection
    • Ishwaran H, Rao JS: Detecting Differentially Expressed Genes in Microarrays Using Bayesian Model Selection. Journal of the American Statistical Association 2003, 98:438-455.
    • (2003) Journal of the American Statistical Association , vol.98 , pp. 438-455
    • Ishwaran, H.1    Rao, J.S.2
  • 17
    • 0036682376 scopus 로고    scopus 로고
    • Meta-analysis of microarrays: Inter-study validation of gene expression profiles reveals pathway dysregulation in prostate cancer
    • Rhodes DR, Barrette TR, Rubin MA, Ghosh D, Chinnaiyan AM: Meta-analysis of microarrays: inter-study validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Research 2002, 62:4427-4433.
    • (2002) Cancer Research , vol.62 , pp. 4427-4433
    • Rhodes, D.R.1    Barrette, T.R.2    Rubin, M.A.3    Ghosh, D.4    Chinnaiyan, A.M.5
  • 18
    • 4944232237 scopus 로고    scopus 로고
    • Combining multiple microarray studies and modeling inter-study variation
    • Choi JK, Yu U, Kim S, Yoo OJ: Combining multiple microarray studies and modeling inter-study variation. Bioinformatics 2003:184-190.
    • (2003) Bioinformatics , pp. 184-190
    • Choi, J.K.1    Yu, U.2    Kim, S.3    Yoo, O.J.4
  • 19
    • 1542309545 scopus 로고    scopus 로고
    • Statistical issues and methods for meta-analysis of microarray data: A case study in prostate cancer
    • Ghosh D, Barette TR, Rhodes D, Chinnaiyan AM: Statistical issues and methods for meta-analysis of microarray data: a case study in prostate cancer. Functional & Integrative Genomics 2003, 3:180-188.
    • (2003) Functional & Integrative Genomics , vol.3 , pp. 180-188
    • Ghosh, D.1    Barette, T.R.2    Rhodes, D.3    Chinnaiyan, A.M.4
  • 20
    • 2442545413 scopus 로고    scopus 로고
    • A cross-study comparison of gene expression studies for the molecular classification of lung cancer
    • Parmigiani G, Garrett-Mayer ES, Anbazhagan R, Gabrielson E. A cross-study comparison of gene expression studies for the molecular classification of lung cancer. Clinical Cancer Research 2004, 10:2922-2927.
    • (2004) Clinical Cancer Research , vol.10 , pp. 2922-2927
    • Parmigiani, G.1    Garrett-Mayer, E.S.2    Anbazhagan, R.3    Gabrielson, E.4
  • 21
    • 13244289883 scopus 로고    scopus 로고
    • Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes
    • Jiang H, Deng Y, Chen H, Tao L, Sha Q, Chen J, Tsai C, Zhang S: Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes. BMC Bioinformatics 2004, 5:81.
    • (2004) BMC Bioinformatics , vol.5 , pp. 81
    • Jiang, H.1    Deng, Y.2    Chen, H.3    Tao, L.4    Sha, Q.5    Chen, J.6    Tsai, C.7    Zhang, S.8
  • 23
    • 25444521278 scopus 로고    scopus 로고
    • Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models
    • Hu P, Greenwood CMT, Beyene J: Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models. BMC Bioinformatics 2005, 6:128.
    • (2005) BMC Bioinformatics , vol.6 , pp. 128
    • Hu, P.1    Greenwood, C.M.T.2    Beyene, J.3
  • 26
  • 28
    • 3543068702 scopus 로고    scopus 로고
    • Microarray platforms - Comparisons and contrasts
    • Hardiman G: Microarray platforms - comparisons and contrasts. Pharmacogenomics 2004, 5:487-502.
    • (2004) Pharmacogenomics , vol.5 , pp. 487-502
    • Hardiman, G.1
  • 29
    • 0000499514 scopus 로고
    • Bayes methods for combining the results of cancer studies in humans and other species
    • DuMouchel WH, Harris JE: Bayes methods for combining the results of cancer studies in humans and other species. Journal of the American Statistical Association 1983, 78:293-315.
    • (1983) Journal of the American Statistical Association , vol.78 , pp. 293-315
    • DuMouchel, W.H.1    Harris, J.E.2
  • 30
    • 0034659898 scopus 로고    scopus 로고
    • Genomics, gene expression and DNA arrays
    • Lockhart DJ, Winzeler EA: Genomics, gene expression and DNA arrays. Nature 2000, 405:827-836.
    • (2000) Nature , vol.405 , pp. 827-836
    • Lockhart, D.J.1    Winzeler, E.A.2
  • 31
    • 0034807713 scopus 로고    scopus 로고
    • Analyzing gene expression data from DNA microarrays to identify candidate genes
    • Wu TD: Analyzing gene expression data from DNA microarrays to identify candidate genes. Journal of Pathology 2001, 195:53-65.
    • (2001) Journal of Pathology , vol.195 , pp. 53-65
    • Wu, T.D.1
  • 32
    • 0036262130 scopus 로고    scopus 로고
    • Microarray technologies - An overview
    • Hardiman G: Microarray technologies - an overview. Pharmacogenomics 2002, 3:293-297.
    • (2002) Pharmacogenomics , vol.3 , pp. 293-297
    • Hardiman, G.1
  • 33
    • 0035237108 scopus 로고    scopus 로고
    • DNA microarrays. History and overview
    • Southern EM: DNA microarrays. History and overview. Methods Mol Biol 2000, 170: 1-15.
    • (2000) Methods Mol Biol , vol.170 , pp. 1-15
    • Southern, E.M.1
  • 34
    • 0036376993 scopus 로고    scopus 로고
    • Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments
    • Dudoit S, Yang YH, Callow MJ, Speed TP: Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statistica Sinica 2002, 12:111-139.
    • (2002) Statistica Sinica , vol.12 , pp. 111-139
    • Dudoit, S.1    Yang, Y.H.2    Callow, M.J.3    Speed, T.P.4
  • 36
    • 0004182828 scopus 로고    scopus 로고
    • Monte Carlo Strategies in Scientific Computing
    • New York, Springer-Verlag
    • Liu JS: Monte Carlo Strategies in Scientific Computing. New York, Springer-Verlag; 2001.
    • (2001)
    • Liu, J.S.1
  • 37
    • 0001677717 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 B 1995, 85:289-300.
    • (1995) Journal of the Royal Statistical Society B , vol.85 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 40
    • 0041423883 scopus 로고    scopus 로고
    • SAM Thresholding and False Discovery Rates for Detecting Differential Gene Expression in DNA Microarrays
    • In Edited by: Parmigiani G, Garrett ES, Irizarry RA, Zeger SL. Springer, NY
    • Storey JS, Tibshirani R: SAM Thresholding and False Discovery Rates for Detecting Differential Gene Expression in DNA Microarrays. In The Analysis of Gene Expression Data: Methods and Software Edited by: Parmigiani G, Garrett ES, Irizarry RA, Zeger SL. Springer, NY; 2003.
    • (2003) The Analysis of Gene Expression Data: Methods and Software
    • Storey, J.S.1    Tibshirani, R.2
  • 41
    • 0036020944 scopus 로고    scopus 로고
    • Operating characteristics and extensions of the false discovery rate procedure
    • Genovese C, Wasserman L: Operating characteristics and extensions of the false discovery rate procedure. Journal of the Royal Statistical Society B 2002, 64:499-518.
    • (2002) Journal of the Royal Statistical Society B , vol.64 , pp. 499-518
    • Genovese, C.1    Wasserman, L.2
  • 42
    • 8844270991 scopus 로고    scopus 로고
    • Determining and analyzing differentially expressed genes from cDNA microarray experiments with complementary designs
    • Conlon EM, Eichenberger P, Liu JS: Determining and analyzing differentially expressed genes from cDNA microarray experiments with complementary designs. Journal of Multivariate Analysis 2004, 90:1-18.
    • (2004) Journal of Multivariate Analysis , vol.90 , pp. 1-18
    • Conlon, E.M.1    Eichenberger, P.2    Liu, J.S.3
  • 43
    • 0035752668 scopus 로고    scopus 로고
    • Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data
    • Schadt EE, Li C, Ellis B, Wong WH: Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. J CellBiochem Suppl 2001, 37:120-125.
    • (2001) J CellBiochem Suppl , vol.37 , pp. 120-125
    • Schadt, E.E.1    Li, C.2    Ellis, B.3    Wong, W.H.4
  • 44
    • 84874652450 scopus 로고    scopus 로고
    • The BUGS Project
    • The BUGS Project [http://www.mrc-bsu.cam.ac.uk/bugs]


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.