메뉴 건너뛰기




Volumn 8, Issue 1, 2008, Pages 43-53

A Bayesian mixture model for metaanalysis of microarray studies

Author keywords

Bayesian statistics; Metaanalysis; Microarray data; Mixture model

Indexed keywords

COMPLEMENTARY DNA;

EID: 37749031194     PISSN: 1438793X     EISSN: 14387948     Source Type: Journal    
DOI: 10.1007/s10142-007-0058-3     Document Type: Article
Times cited : (12)

References (53)
  • 1
    • 0034948896 scopus 로고    scopus 로고
    • A Bayesian framework for the analysis of microarray expression data: Reguralized t test and statistical inferences of gene changes
    • Baldi P, Long AD (2001) A Bayesian framework for the analysis of microarray expression data: Reguralized 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
  • 2
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc B 85:289-300
    • (1995) J R Stat Soc B , vol.85 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 3
    • 33749626257 scopus 로고    scopus 로고
    • A Laplace mixture model for identification of differential expression in microarray experiments
    • Bhowmick D, Davison AC, Goldstein DR, Ruffieux Y (2006) A Laplace mixture model for identification of differential expression in microarray experiments. Biostatistics 7:630-641
    • (2006) Biostatistics , vol.7 , pp. 630-641
    • Bhowmick, D.1    Davison, A.C.2    Goldstein, D.R.3    Ruffieux, Y.4
  • 4
    • 0036401627 scopus 로고    scopus 로고
    • Bayesian hierarchical model for identifying changes in gene expression from microarray experiments
    • Broët P, Richardson S, Radvanyi F (2002) Bayesian hierarchical model for identifying changes in gene expression from microarray experiments. J Comput Biol 9:671-683
    • (2002) J Comput Biol , vol.9 , pp. 671-683
    • Broët, P.1    Richardson, S.2    Radvanyi, F.3
  • 5
    • 4944232237 scopus 로고    scopus 로고
    • Combining multiple microarray studies and modeling inter-study variation
    • Choi JK, Yu U, Kim S, Yoo OJ (2003) Combining multiple microarray studies and modeling inter-study variation. Bioinformatics Suppl 19:i84-i90
    • (2003) Bioinformatics Suppl , vol.19
    • Choi, J.K.1    Yu, U.2    Kim, S.3    Yoo, O.J.4
  • 6
    • 8844270991 scopus 로고    scopus 로고
    • Determining and analyzing differentially expressed genes from cDNA microarray experiments with complementary designs
    • Conlon EM, Eichenberger P, Liu JS (2004) Determining and analyzing differentially expressed genes from cDNA microarray experiments with complementary designs. JMVA 90:1-18
    • (2004) JMVA , vol.90 , pp. 1-18
    • Conlon, E.M.1    Eichenberger, P.2    Liu, J.S.3
  • 7
    • 33747017793 scopus 로고    scopus 로고
    • Bayesian models for pooling microarray studies with multiple sources of replications
    • Conlon EM, Song JJ, Liu JS (2006) Bayesian models for pooling microarray studies with multiple sources of replications. BMC Bioinformatics 7:247
    • (2006) BMC Bioinformatics , vol.7 , pp. 247
    • Conlon, E.M.1    Song, J.J.2    Liu, J.S.3
  • 8
    • 34147103409 scopus 로고    scopus 로고
    • Bayesian meta-analysis models for microarray data: A comparative study
    • Conlon EM, Song JJ, Liu A (2007) Bayesian meta-analysis models for microarray data: A comparative study. BMC Bioinformatics 8:80
    • (2007) BMC Bioinformatics , vol.8 , pp. 80
    • Conlon, E.M.1    Song, J.J.2    Liu, A.3
  • 9
    • 18444401138 scopus 로고    scopus 로고
    • A Bayesian mixture model for differential gene expression
    • Do KA, Müller P, Tang F (2005) A Bayesian mixture model for differential gene expression. J R Stat Soc C 54:627-644
    • (2005) J R Stat Soc C , vol.54 , pp. 627-644
    • Do, K.A.1    Müller, P.2    Tang, F.3
  • 10
    • 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 (2002) Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Stat Sin 12:111-139
    • (2002) Stat Sin , vol.12 , pp. 111-139
    • Dudoit, S.1    Yang, Y.H.2    Callow, M.J.3    Speed, T.P.4
  • 13
    • 0036020944 scopus 로고    scopus 로고
    • Operating characteristics and extensions of the false discovery rate procedure
    • Genovese C, Wasserman L (2002) Operating characteristics and extensions of the false discovery rate procedure. J R Stat Soc B 64:499-518
    • (2002) J R Stat Soc B , vol.64 , pp. 499-518
    • Genovese, C.1    Wasserman, L.2
  • 14
    • 10844295316 scopus 로고    scopus 로고
    • Bayesian and frequentist multiple testing
    • In: Bernardo JM, Bayarri JM, Berger JO, Dawid AP, Heckerman D, Smith AFM, West M (eds) Oxford University Press, Oxford
    • Genovese C, Wasserman L (2003) Bayesian and frequentist multiple testing. In: Bernardo JM, Bayarri JM, Berger JO, Dawid AP, Heckerman D, Smith AFM, West M (eds) Bayesian statistics 7. Oxford University Press, Oxford, pp 145-162
    • (2003) Bayesian Statistics 7 , pp. 145-162
    • Genovese, C.1    Wasserman, L.2
  • 15
    • 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 (2003) Statistical issues and methods for meta-analysis of microarray data: A case study in prostate cancer. Funct Integr Genomics 3:180-188
    • (2003) Funct Integr Genomics , vol.3 , pp. 180-188
    • Ghosh, D.1    Barette, T.R.2    Rhodes, D.3    Chinnaiyan, A.M.4
  • 17
    • 25444521278 scopus 로고    scopus 로고
    • Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models
    • Hu P, Greenwood CMT, Beyene J (2005a) Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models. BMC Bioinformatics 6:128
    • (2005) BMC Bioinformatics , vol.6 , pp. 128
    • Hu, P.1    Greenwood, C.M.T.2    Beyene, J.3
  • 18
    • 25144521453 scopus 로고    scopus 로고
    • Practical FDR-based sample size calculations in microarray experiments
    • Hu J, Zou F, Wright FA (2005b) Practical FDR-based sample size calculations in microarray experiments. Bioinformatics 21:3264-3272
    • (2005) Bioinformatics , vol.21 , pp. 3264-3272
    • Hu, J.1    Zou, F.2    Wright, F.A.3
  • 19
    • 0036489048 scopus 로고    scopus 로고
    • Bayesian models for gene expression with DNA microarray data
    • Ibrahim JG, Chen M-H, Gray RJ (2002) Bayesian models for gene expression with DNA microarray data. J Am Stat Assoc 97:88-99
    • (2002) J Am Stat Assoc , vol.97 , pp. 88-99
    • Ibrahim, J.G.1    Chen, M.-H.2    Gray, R.J.3
  • 20
    • 0042744696 scopus 로고    scopus 로고
    • Detecting differentially expressed genes in microarrays using Bayesian model selection
    • Ishwaran H, Rao JS (2003) Detecting differentially expressed genes in microarrays using Bayesian model selection. J Am Stat Assoc 98:438-455
    • (2003) J Am Stat Assoc , vol.98 , pp. 438-455
    • Ishwaran, H.1    Rao, J.S.2
  • 21
    • 22944431540 scopus 로고    scopus 로고
    • Spike and slab gene selection for multipgroup microarray data
    • Ishwaran H, Rao JS (2005) Spike and slab gene selection for multipgroup microarray data. J Am Stat Assoc 100:764-780
    • (2005) J Am Stat Assoc , vol.100 , pp. 764-780
    • Ishwaran, H.1    Rao, J.S.2
  • 23
    • 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 (2004) Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes. BMC Bioinformatics 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
  • 24
    • 33745654577 scopus 로고    scopus 로고
    • Identifying differentially expressed genes in meta-analysis via Bayesian model-based clustering
    • Jung YY, Oh MS, Shin DW, Kang SH, Oh HS (2006) Identifying differentially expressed genes in meta-analysis via Bayesian model-based clustering. Biom J 48:435-450
    • (2006) Biom J , vol.48 , pp. 435-450
    • Jung, Y.Y.1    Oh, M.S.2    Shin, D.W.3    Kang, S.H.4    Oh, H.S.5
  • 25
    • 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 (2003) On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles. Stat Med 22:3899-3914
    • (2003) Stat Med , vol.22 , pp. 3899-3914
    • Kendziorski, C.M.1    Newton, M.A.2    Lan, H.3    Gould, M.N.4
  • 28
    • 17244361971 scopus 로고    scopus 로고
    • Hierarchical bayes models for cDNA microarray gene expression
    • Lönnstedt I, Britton T (2005) Hierarchical bayes models for cDNA microarray gene expression. Biostatistics 6:279-291
    • (2005) Biostatistics , vol.6 , pp. 279-291
    • Lönnstedt, I.1    Britton, T.2
  • 29
    • 0036012343 scopus 로고    scopus 로고
    • Replicated microarray data
    • Lönnstedt I, Speed TP (2002) Replicated microarray data. Stat Sin 12:31-46
    • (2002) Stat Sin , vol.12 , pp. 31-46
    • Lönnstedt, I.1    Speed, T.P.2
  • 30
    • 37749049067 scopus 로고    scopus 로고
    • London. Cited 13 Sep 2003 Imperial College School of Medicine
    • Lunn DJ (2003) WBDevDJLTruncatedNormal documentation. Imperial College School of Medicine, London. http://www.winbugs-development.org.uk. Cited 13 Sep 2003
    • (2003) WBDevDJLTruncatedNormal Documentation
    • Lunn, D.J.1
  • 32
    • 33646052085 scopus 로고    scopus 로고
    • Pooling information across different studies and oligonucleotide microarray chip types to identify prognostic genes for lung cancer
    • In: Shoemaker JS, Lin SM (eds) Springer, New York
    • Morris JS, Yin G, Baggerly KA, Wu C, Zhang L (2005) Pooling information across different studies and oligonucleotide microarray chip types to identify prognostic genes for lung cancer. In: Shoemaker JS, Lin SM (eds) Methods of microarray data analysis IV. Springer, New York, pp 51-66
    • (2005) Methods of Microarray Data Analysis IV , pp. 51-66
    • Morris, J.S.1    Yin, G.2    Baggerly, K.A.3    Wu, C.4    Zhang, L.5
  • 33
    • 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 (2001) On differential variability of expression ratios: Improving statistical inference about gene expression changes from microarray data. J Comput Biol 8:37-52
    • (2001) J Comput Biol , 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
  • 34
    • 4444235995 scopus 로고    scopus 로고
    • Detecting differential gene expression with a semiparametric hierarchical mixture method
    • Newton MA, Noueiry A, Sarkar D, 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
  • 35
    • 33747874717 scopus 로고    scopus 로고
    • Combining multiple microarrays in the presence of controlling variables
    • Park T,Yi SG, Shin YK, Lee S (2006) Combining multiple microarrays in the presence of controlling variables. Bioinformatics 22:1682-1689
    • (2006) Bioinformatics , vol.22 , pp. 1682-1689
    • Park, T.1    Yi, S.G.2    Shin, Y.K.3    Lee, S.4
  • 36
    • 0036433548 scopus 로고    scopus 로고
    • A statistical framework for expression-based molecular classification in cancer
    • Parmigiani G, Garrett ES, Anbazhagan R, Gabrielson E (2002) A statistical framework for expression-based molecular classification in cancer. J R Stat Soc B 64:717-736
    • (2002) J R Stat Soc B , vol.64 , pp. 717-736
    • Parmigiani, G.1    Garrett, E.S.2    Anbazhagan, R.3    Gabrielson, E.4
  • 37
    • 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 (2004) A cross-study comparison of gene expression studies for the molecular classification of lung cancer. Clin Cancer Res 10:2922-2927
    • (2004) Clin Cancer Res , vol.10 , pp. 2922-2927
    • Parmigiani, G.1    Garrett-Mayer, E.S.2    Anbazhagan, R.3    Gabrielson, E.4
  • 38
    • 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 (2002) Meta-analysis of microarrays: Inter-study validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res 62:4427-4433
    • (2002) Cancer Res , vol.62 , pp. 4427-4433
    • Rhodes, D.R.1    Barrette, T.R.2    Rubin, M.A.3    Ghosh, D.4    Chinnaiyan, A.M.5
  • 40
    • 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 (2001) Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. J Cell Biochem Suppl 37:120-125
    • (2001) J Cell Biochem Suppl , vol.37 , pp. 120-125
    • Schadt, E.E.1    Li, C.2    Ellis, B.3    Wong, W.H.4
  • 41
    • 20044395334 scopus 로고    scopus 로고
    • Prognostic meta-signature of breast cancer developed by two-stage mixture modeling of microarray data
    • Shen R, Ghosh D, Chinnaiyan AM (2004) Prognostic meta-signature of breast cancer developed by two-stage mixture modeling of microarray data. BMC Genomics 5:94
    • (2004) BMC Genomics , vol.5 , pp. 94
    • Shen, R.1    Ghosh, D.2    Chinnaiyan, A.M.3
  • 42
    • 0003818292 scopus 로고    scopus 로고
    • MRC Biostatistics Unit Cambridge, and Imperial College School of Medicine, London. Cited 1 Jan 2003
    • Spiegelhalter DJ, Thomas A, Best NG (2003) WinBUGS Version 1.4, User Manual. MRC Biostatistics Unit, Cambridge, and Imperial College School of Medicine, London. http://www.mrc-bsu.cam.ac.uk/bugs. Cited 1 Jan 2003
    • (2003) WinBUGS Version 1.4, User Manual
    • Spiegelhalter, D.J.1    Thomas, A.2    Best, N.G.3
  • 43
    • 0037478724 scopus 로고    scopus 로고
    • Meta-analysis: Past and present challenges
    • In: Stangl DK, Berry DA (eds) Dekker, New York
    • Stangl DK, Berry DA (2000) Meta-analysis: Past and present challenges. In: Stangl DK, Berry DA (eds) Meta-analysis in medicine and health policy. Dekker, New York, pp 1-28
    • (2000) Meta-analysis in Medicine and Health Policy , pp. 1-28
    • Stangl, D.K.1    Berry, D.A.2
  • 45
    • 0036020892 scopus 로고    scopus 로고
    • A direct approach to false discovery rates
    • Storey JD (2002) A direct approach to false discovery rates. J R Stat Soc B 64:479-498
    • (2002) J R Stat Soc B , vol.64 , pp. 479-498
    • Storey, J.D.1
  • 46
    • 0041423883 scopus 로고    scopus 로고
    • SAM thresholding and false discovery rates for detecting differential gene expression in DNA microarrays
    • In: Parmigiani G, Garrett ES, Irizarry RA, Zeger SL (eds) Springer, New York
    • Storey JS, Tibshirani R (2003) SAM thresholding and false discovery rates for detecting differential gene expression in DNA microarrays. In: Parmigiani G, Garrett ES, Irizarry RA, Zeger SL (eds) The analysis of gene expression data: Methods and software. Springer, New York, pp 272-290
    • (2003) The Analysis of Gene Expression Data: Methods and Software , pp. 272-290
    • Storey, J.S.1    Tibshirani, R.2
  • 47
    • 0037975700 scopus 로고    scopus 로고
    • Bayesian analysis of gene expression levels: Statistical quantification of relative mRNA level across multiple treatments or samples
    • research007 1.1-71.16
    • Townsend JP, Hartl DL (2002) Bayesian analysis of gene expression levels: Statistical quantification of relative mRNA level across multiple treatments or samples. Genome Biol 3:rEsearch0071.1-71.16
    • (2002) Genome Biol , vol.3
    • Townsend, J.P.1    Hartl, D.L.2
  • 48
    • 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 (2001) Issues in cDNA microarray analysis: Quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res 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
  • 49
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98:5116-5121
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 50
    • 0029966525 scopus 로고    scopus 로고
    • Bayesian meta-analysis, with application to studies of ETS and lung cancer
    • Tweedie RL, Scott DJ, Biggerstaff BJ, Mengersen KL (1996) Bayesian meta-analysis, with application to studies of ETS and lung cancer. Lung Cancer 14 Suppl 1:S171-S194
    • (1996) Lung Cancer , vol.14 , Issue.SUPPL. 1
    • Tweedie, R.L.1    Scott, D.J.2    Biggerstaff, B.J.3    Mengersen, K.L.4
  • 51
    • 10244224128 scopus 로고    scopus 로고
    • Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: A meta-analysis of three microarray studies
    • Wang J, Coombes KR, Highsmith WE, Keating MJ, Abruzzo LV (2004) Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: A meta-analysis of three microarray studies. Bioinformatics 20:3166-3178
    • (2004) Bioinformatics , vol.20 , pp. 3166-3178
    • Wang, J.1    Coombes, K.R.2    Highsmith, W.E.3    Keating, M.J.4    Abruzzo, L.V.5
  • 52
    • 27844594381 scopus 로고    scopus 로고
    • Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes
    • Warnat P, Eils R, Brors B (2005) Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes. BMC Bioinformatics 6:265
    • (2005) BMC Bioinformatics , vol.6 , pp. 265
    • Warnat, P.1    Eils, R.2    Brors, B.3
  • 53
    • 27544492493 scopus 로고    scopus 로고
    • Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data
    • Xu L, Tan AC, Naiman DQ, Geman D, Winslow RL (2005) Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data. Bioinformatics 21:3905-3911
    • (2005) Bioinformatics , vol.21 , pp. 3905-3911
    • Xu, L.1    Tan, A.C.2    Naiman, D.Q.3    Geman, D.4    Winslow, R.L.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.