메뉴 건너뛰기




Volumn 12, Issue , 2011, Pages

Multiple testing for gene sets from microarray experiments

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGIC FUNCTIONS; CLINICAL OUTCOME; FALSE DISCOVERY RATE; GENE SET ENRICHMENT ANALYSIS; IDENTIFICATION OF INDIVIDUALS; MICROARRAY DATA SETS; MICROARRAY EXPERIMENTS; MULTIPLE TESTING;

EID: 79957498511     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-209     Document Type: Article
Times cited : (4)

References (46)
  • 1
    • 0032919364 scopus 로고    scopus 로고
    • KEGG: Kyoto Encyclopedia of Genes and Genomes
    • 10.1093/nar/27.1.29, 148090, 9847135
    • Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 1999, 27:29-34. 10.1093/nar/27.1.29, 148090, 9847135.
    • (1999) Nucleic Acids Res , vol.27 , pp. 29-34
    • Ogata, H.1    Goto, S.2    Sato, K.3    Fujibuchi, W.4    Bono, H.5    Kanehisa, M.6
  • 3
    • 63449107173 scopus 로고    scopus 로고
    • A general modular framework for gene set enrichment analysis
    • Ackermann M, Strimmer K. A general modular framework for gene set enrichment analysis. BMC Bioinformatics 2009, 88:365-411.
    • (2009) BMC Bioinformatics , vol.88 , pp. 365-411
    • Ackermann, M.1    Strimmer, K.2
  • 5
    • 0345832338 scopus 로고    scopus 로고
    • A global test for groups of genes: testing association with a clinical outcome
    • 10.1093/bioinformatics/btg382, 14693814
    • Goeman JJ, van de Geer SA, de Kort F, van Houwelingen HC. A global test for groups of genes: testing association with a clinical outcome. Bioinformatics 2004, 20:93-99. 10.1093/bioinformatics/btg382, 14693814.
    • (2004) Bioinformatics , vol.20 , pp. 93-99
    • Goeman, J.J.1    van de Geer, S.A.2    de Kort, F.3    van Houwelingen, H.C.4
  • 8
    • 22944444171 scopus 로고    scopus 로고
    • Testing differential gene expression in functional groups. Goeman's global test versus an ANCOVA approach
    • Mansmann U, Meister R. Testing differential gene expression in functional groups. Goeman's global test versus an ANCOVA approach. Methods of Inf Med 2005, 44:449-453.
    • (2005) Methods of Inf Med , vol.44 , pp. 449-453
    • Mansmann, U.1    Meister, R.2
  • 9
    • 18744389489 scopus 로고    scopus 로고
    • Significance analysis of functional categories in gene expression studies: a structured permutation approach
    • 10.1093/bioinformatics/bti260, 15647293
    • Barry WT, Nobel AB, Wright F. Significance analysis of functional categories in gene expression studies: a structured permutation approach. Bioinformatics 2005, 21:1943-1949. 10.1093/bioinformatics/bti260, 15647293.
    • (2005) Bioinformatics , vol.21 , pp. 1943-1949
    • Barry, W.T.1    Nobel, A.B.2    Wright, F.3
  • 10
    • 33750007469 scopus 로고    scopus 로고
    • A multivariate approach for integrating genome-wide expression data and biological knowledge
    • 10.1093/bioinformatics/btl401, 2813864, 16877751
    • Kong SW, Pu WT, Park PJ. A multivariate approach for integrating genome-wide expression data and biological knowledge. Bioinformatics 2006, 22:2373-2380. 10.1093/bioinformatics/btl401, 2813864, 16877751.
    • (2006) Bioinformatics , vol.22 , pp. 2373-2380
    • Kong, S.W.1    Pu, W.T.2    Park, P.J.3
  • 11
    • 38349182215 scopus 로고    scopus 로고
    • Identification of differentially expressed gene categories in microarray studies using non-parametric multivariate analysis
    • 10.1093/bioinformatics/btm583, 18042553
    • Nettleton D, Recknor J, Reecy JM. Identification of differentially expressed gene categories in microarray studies using non-parametric multivariate analysis. Bioinformatics 2008, 24:192-201. 10.1093/bioinformatics/btm583, 18042553.
    • (2008) Bioinformatics , vol.24 , pp. 192-201
    • Nettleton, D.1    Recknor, J.2    Reecy, J.M.3
  • 12
    • 60149104156 scopus 로고    scopus 로고
    • A statistical framework for testing functional categories in microarray data
    • Barry WT, Nobel AB, Wright F. A statistical framework for testing functional categories in microarray data. Annals of Applied Statistics 2008, 2:286-315.
    • (2008) Annals of Applied Statistics , vol.2 , pp. 286-315
    • Barry, W.T.1    Nobel, A.B.2    Wright, F.3
  • 13
    • 63549122405 scopus 로고    scopus 로고
    • Multivariate analysis of variance test for gene set analysis
    • 10.1093/bioinformatics/btp098, 19254923
    • Tsai C-A, Chen JJ. Multivariate analysis of variance test for gene set analysis. Bioinformatics 2009, 25:897-903. 10.1093/bioinformatics/btp098, 19254923.
    • (2009) Bioinformatics , vol.25 , pp. 897-903
    • Tsai, C.-A.1    Chen, J.J.2
  • 14
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini Y, Hochber Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. Series B 1995, 57:289-300.
    • (1995) Journal of the Royal Statistical Society. Series B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochber, Y.2
  • 15
    • 70149113077 scopus 로고    scopus 로고
    • R: A Language and Environment for Statistical Computing
    • ISBN 3-900051-07-0, Development Core Team
    • Development Core Team R: A Language and Environment for Statistical Computing. 2009, ISBN 3-900051-07-0, Development Core Team.
    • (2009)
  • 21
  • 23
    • 42349090022 scopus 로고    scopus 로고
    • Penalized normal likelihood and ridge regularization of correlation and covariance matrices
    • Warton DI. Penalized normal likelihood and ridge regularization of correlation and covariance matrices. Journal of the American Statistical Association 2009, 103:340-349.
    • (2009) Journal of the American Statistical Association , vol.103 , pp. 340-349
    • Warton, D.I.1
  • 24
    • 27844521293 scopus 로고    scopus 로고
    • A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics
    • Schafer J, Strimmer K. A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics. Statistical Applications in Genetics and Molecular Biology 2005, 4:32.
    • (2005) Statistical Applications in Genetics and Molecular Biology , vol.4 , pp. 32
    • Schafer, J.1    Strimmer, K.2
  • 25
    • 0346961488 scopus 로고    scopus 로고
    • A Well-conditioned estimator for large-dimensional covariance matrices
    • Ledoit O, Wolf M. A Well-conditioned estimator for large-dimensional covariance matrices. Journal of Multivariate Analysis 2004, 88:365-411.
    • (2004) Journal of Multivariate Analysis , vol.88 , pp. 365-411
    • Ledoit, O.1    Wolf, M.2
  • 26
    • 0000235653 scopus 로고
    • Some theorems on quadratic forms applied in the study of analysis of variance problems, I. Effect of inequality of variance in the one-way classification
    • Box GEP. Some theorems on quadratic forms applied in the study of analysis of variance problems, I. Effect of inequality of variance in the one-way classification. The Annals of Mathematical Statistics 1995, 25:290-302.
    • (1995) The Annals of Mathematical Statistics , vol.25 , pp. 290-302
    • Box, G.E.P.1
  • 27
    • 67449143322 scopus 로고    scopus 로고
    • Asymptotic and approximate analysis of repeated measuresd esigns under heteroscedasticity
    • Josef Eul Verlag, Lohmar, Kunert J, Trenkler G
    • Brunner E. Asymptotic and approximate analysis of repeated measuresd esigns under heteroscedasticity. mathematical statistics with applications in biometrys 2001, Josef Eul Verlag, Lohmar, Kunert J, Trenkler G.
    • (2001) mathematical statistics with applications in biometrys
    • Brunner, E.1
  • 28
    • 77649330805 scopus 로고    scopus 로고
    • A two sample test for high dimensional data with application to gene-set testing
    • Chen SX, Qin YL. A two sample test for high dimensional data with application to gene-set testing. The Annals of Statistics 2010, 38:808-835.
    • (2010) The Annals of Statistics , vol.38 , pp. 808-835
    • Chen, S.X.1    Qin, Y.L.2
  • 33
    • 77049120689 scopus 로고    scopus 로고
    • X-changing information on X inactivation
    • 10.1016/j.yexcr.2010.01.015, 20083102
    • Barakata TS, Jonkers I, Monkhorst K, Gribnau J. X-changing information on X inactivation. Exp Cell Res 2010, 316:679-687. 10.1016/j.yexcr.2010.01.015, 20083102.
    • (2010) Exp Cell Res , vol.316 , pp. 679-687
    • Barakata, T.S.1    Jonkers, I.2    Monkhorst, K.3    Gribnau, J.4
  • 34
    • 70349694418 scopus 로고    scopus 로고
    • Dosage compensation and gene expression on the mammalian X chromosome: one plus one does not always equal two
    • 10.1007/s10577-009-9063-9, 19802704
    • Prothero KE, Stahl JM, Carrel L. Dosage compensation and gene expression on the mammalian X chromosome: one plus one does not always equal two. Chromosome Res 2009, 17:637-648. 10.1007/s10577-009-9063-9, 19802704.
    • (2009) Chromosome Res , vol.17 , pp. 637-648
    • Prothero, K.E.1    Stahl, J.M.2    Carrel, L.3
  • 35
    • 67649884786 scopus 로고    scopus 로고
    • Gene set enrichment analyses revealed differences in gene expression patterns between males and females
    • 2757739, 19795565
    • Zhang W, Huang RS, Duan S, Dolan ME. Gene set enrichment analyses revealed differences in gene expression patterns between males and females. In Silico Biol 2009, 9:55-63. 2757739, 19795565.
    • (2009) In Silico Biol , vol.9 , pp. 55-63
    • Zhang, W.1    Huang, R.S.2    Duan, S.3    Dolan, M.E.4
  • 36
    • 70350761428 scopus 로고    scopus 로고
    • ACAT2 and human hepatic cholesterol metabolism: identification of important gender-related differences in nor-molipidemic, non-obese Chinese patients
    • 10.1016/j.atherosclerosis.2009.04.010, 2784173, 19467657
    • Parini P, Jiang ZY, Einarsson C, Eggertsen G, Zhang SD, Rudel LL, Han TQ, Eriksson M. ACAT2 and human hepatic cholesterol metabolism: identification of important gender-related differences in nor-molipidemic, non-obese Chinese patients. Atherosclerosis 2009, 207:266-271. 10.1016/j.atherosclerosis.2009.04.010, 2784173, 19467657.
    • (2009) Atherosclerosis , vol.207 , pp. 266-271
    • Parini, P.1    Jiang, Z.Y.2    Einarsson, C.3    Eggertsen, G.4    Zhang, S.D.5    Rudel, L.L.6    Han, T.Q.7    Eriksson, M.8
  • 38
    • 63849234720 scopus 로고    scopus 로고
    • Determination of physiological plasma pentraxin 3 (PTX3) levels in healthy populations
    • 10.1515/CCLM.2009.110, 19327124
    • Yamasaki K, Kurimura M, Kasai T, Sagara M, Kodama T, Inoue K. Determination of physiological plasma pentraxin 3 (PTX3) levels in healthy populations. Clin Chem Lab Med 2009, 47:471-477. 10.1515/CCLM.2009.110, 19327124.
    • (2009) Clin Chem Lab Med , vol.47 , pp. 471-477
    • Yamasaki, K.1    Kurimura, M.2    Kasai, T.3    Sagara, M.4    Kodama, T.5    Inoue, K.6
  • 39
    • 55049096678 scopus 로고    scopus 로고
    • Role of sex and time of blood sampling in SOD1 and SOD2 expression variability
    • 10.1016/j.clinbiochem.2008.08.064, 18775420
    • Khymenets O, Covas MI, Farre M, Langohr K, Fito M, de la Torre R. Role of sex and time of blood sampling in SOD1 and SOD2 expression variability. Clin Biochem 2008, 41:1348-1354. 10.1016/j.clinbiochem.2008.08.064, 18775420.
    • (2008) Clin Biochem , vol.41 , pp. 1348-1354
    • Khymenets, O.1    Covas, M.I.2    Farre, M.3    Langohr, K.4    Fito, M.5    de la Torre, R.6
  • 40
    • 42749084082 scopus 로고    scopus 로고
    • The impact of p53 and p73 on aneuploidy and cancer
    • 10.1016/j.tcb.2008.03.003, 18406616
    • Tomasini R, Mark TW, Melino G. The impact of p53 and p73 on aneuploidy and cancer. Trends Cell Biol 2008, 18:244-252. 10.1016/j.tcb.2008.03.003, 18406616.
    • (2008) Trends Cell Biol , vol.18 , pp. 244-252
    • Tomasini, R.1    Mark, T.W.2    Melino, G.3
  • 41
    • 0029793416 scopus 로고    scopus 로고
    • Repression of interleukin-2 and interleukin- 4 promoters by tumor suppressor protein p53
    • 10.1089/jir.1996.16.595, 8877730
    • Pesch J, Brehm U, Staib C, Grummt F. Repression of interleukin-2 and interleukin- 4 promoters by tumor suppressor protein p53. J Interferon Cytokine Res 1996, 16:595-600. 10.1089/jir.1996.16.595, 8877730.
    • (1996) J Interferon Cytokine Res , vol.16 , pp. 595-600
    • Pesch, J.1    Brehm, U.2    Staib, C.3    Grummt, F.4
  • 42
    • 0001080345 scopus 로고    scopus 로고
    • Identification of an additional p53-responsive site in the human epidermal growth factor receptor gene promotor
    • 10.1038/sj.onc.1201264, 9285564
    • Sheikh MS, Carrier F, Johnson AC, Ogdon SE, Fornace AJ. Identification of an additional p53-responsive site in the human epidermal growth factor receptor gene promotor. Oncogene 1997, 15:1095-1101. 10.1038/sj.onc.1201264, 9285564.
    • (1997) Oncogene , vol.15 , pp. 1095-1101
    • Sheikh, M.S.1    Carrier, F.2    Johnson, A.C.3    Ogdon, S.E.4    Fornace, A.J.5
  • 43
    • 34347209447 scopus 로고    scopus 로고
    • NGF-mediated transcriptional targets of p53 in PC12 neuronal differentiation
    • 10.1186/1471-2164-8-139, 1894799, 17540029
    • Brynczka C, Labhart P, Merrick BA. NGF-mediated transcriptional targets of p53 in PC12 neuronal differentiation. BMC Genomics 2007, 8:139. 10.1186/1471-2164-8-139, 1894799, 17540029.
    • (2007) BMC Genomics , vol.8 , pp. 139
    • Brynczka, C.1    Labhart, P.2    Merrick, B.A.3
  • 44
    • 34249043939 scopus 로고    scopus 로고
    • Negative regulation of chemokine receptor CXCR4 by tumor suppressor p53 in breast cancer cells: implications of p53 mutation or isoform expression on breast cancer cell invasion
    • 10.1038/sj.onc.1210120, 17130833
    • Mehta SA, Christopherson KW, Bhat-Nakshatri P, Goulet RJ, Broxmeyer HE, Kopelovich L, Nakshatri H. Negative regulation of chemokine receptor CXCR4 by tumor suppressor p53 in breast cancer cells: implications of p53 mutation or isoform expression on breast cancer cell invasion. Oncogene 2007, 26:3329-3337. 10.1038/sj.onc.1210120, 17130833.
    • (2007) Oncogene , vol.26 , pp. 3329-3337
    • Mehta, S.A.1    Christopherson, K.W.2    Bhat-Nakshatri, P.3    Goulet, R.J.4    Broxmeyer, H.E.5    Kopelovich, L.6    Nakshatri, H.7
  • 45
    • 0034601013 scopus 로고    scopus 로고
    • The GTPase rho controls a p53-dependent survival check-point during thymopoiesis
    • 10.1084/jem.192.1.77, 1887705, 10880528
    • Costello PS, Cleverley SC, Galandrini R, Henning SW, Cantrell DA. The GTPase rho controls a p53-dependent survival check-point during thymopoiesis. J Exp Med 2000, 192:77-85. 10.1084/jem.192.1.77, 1887705, 10880528.
    • (2000) J Exp Med , vol.192 , pp. 77-85
    • Costello, P.S.1    Cleverley, S.C.2    Galandrini, R.3    Henning, S.W.4    Cantrell, D.A.5
  • 46
    • 51649114848 scopus 로고    scopus 로고
    • Kinetics of repression by modified p53 on the PDGF beta-receptor promoter
    • 10.1002/ijc.23735, 18697203
    • Yang W, Wetterskog D, Matsumoto Y, Funa K. Kinetics of repression by modified p53 on the PDGF beta-receptor promoter. Int J Cancer 2008, 123:2020-2030. 10.1002/ijc.23735, 18697203.
    • (2008) Int J Cancer , vol.123 , pp. 2020-2030
    • Yang, W.1    Wetterskog, D.2    Matsumoto, Y.3    Funa, K.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.