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Volumn 4, Issue 11, 2009, Pages

Identifying Gene Interaction Enrichment for Gene Expression Data

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[No Author keywords available]

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VASCULOTROPIN A;

EID: 77951245218     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0008064     Document Type: Article
Times cited : (22)

References (32)
  • 1
    • 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 U S A 98: 5116-5121.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 2
    • 0038238080 scopus 로고    scopus 로고
    • Statistical methods for ranking differentially expressed genes
    • Broberg P, (2003) Statistical methods for ranking differentially expressed genes. Genome Biol 4: R41.
    • (2003) Genome Biol , vol.4
    • Broberg, P.1
  • 3
    • 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, Long AD, (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
  • 4
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
    • Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al.(2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102: 15545-15550.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 15545-15550
    • Subramanian, A.1    Tamayo, P.2    Mootha, V.K.3    Mukherjee, S.4    Ebert, B.L.5
  • 6
    • 34249663294 scopus 로고    scopus 로고
    • Analyzing gene expression data in terms of gene sets: methodological issues
    • Goeman JJ, Buhlmann P, (2007) Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics 23: 980-987.
    • (2007) Bioinformatics , vol.23 , pp. 980-987
    • Goeman, J.J.1    Buhlmann, P.2
  • 7
    • 0038054341 scopus 로고    scopus 로고
    • PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
    • Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, et al.(2003) PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 34: 267-273.
    • (2003) Nat Genet , vol.34 , pp. 267-273
    • Mootha, V.K.1    Lindgren, C.M.2    Eriksson, K.F.3    Subramanian, A.4    Sihag, S.5
  • 10
    • 22944444171 scopus 로고    scopus 로고
    • Testing differential gene expression in functional groups. Goeman's global test versus an ANCOVA approach
    • Mansmann U, Meister R, (2005) Testing differential gene expression in functional groups. Goeman's global test versus an ANCOVA approach. Methods Inf Med 44: 449-453.
    • (2005) Methods Inf Med , vol.44 , pp. 449-453
    • Mansmann, U.1    Meister, R.2
  • 11
    • 63549122405 scopus 로고    scopus 로고
    • Multivariate analysis of variance test for gene set analysis
    • Tsai CA, Chen JJ, (2009) Multivariate analysis of variance test for gene set analysis. Bioinformatics 25: 897-903.
    • (2009) Bioinformatics , vol.25 , pp. 897-903
    • Tsai, C.A.1    Chen, J.J.2
  • 12
    • 0032928542 scopus 로고    scopus 로고
    • Loci on chromosomes 2 (NIDDM1) and 15 interact to increase susceptibility to diabetes in Mexican Americans
    • Cox NJ, Frigge M, Nicolae DL, Concannon P, Hanis CL, et al.(1999) Loci on chromosomes 2 (NIDDM1) and 15 interact to increase susceptibility to diabetes in Mexican Americans. Nat Genet 21: 213-215.
    • (1999) Nat Genet , vol.21 , pp. 213-215
    • Cox, N.J.1    Frigge, M.2    Nicolae, D.L.3    Concannon, P.4    Hanis, C.L.5
  • 13
    • 19944432169 scopus 로고    scopus 로고
    • Oligogenic combinations associated with breast cancer risk in women under 53 years of age
    • Aston CE, Ralph DA, Lalo DP, Manjeshwar S, Gramling BA, et al.(2005) Oligogenic combinations associated with breast cancer risk in women under 53 years of age. Hum Genet 116: 208-221.
    • (2005) Hum Genet , vol.116 , pp. 208-221
    • Aston, C.E.1    Ralph, D.A.2    Lalo, D.P.3    Manjeshwar, S.4    Gramling, B.A.5
  • 14
    • 48349142136 scopus 로고    scopus 로고
    • Class-specific correlations of gene expressions: identification and their effects on clustering analyses
    • Zhang J, Li J, Deng H, (2008) Class-specific correlations of gene expressions: identification and their effects on clustering analyses. Am J Hum Genet 83: 269-277.
    • (2008) Am J Hum Genet , vol.83 , pp. 269-277
    • Zhang, J.1    Li, J.2    Deng, H.3
  • 15
    • 0042881041 scopus 로고    scopus 로고
    • Mathematical multi-locus approaches to localizing complex human trait genes
    • Hoh J, Ott J, (2003) Mathematical multi-locus approaches to localizing complex human trait genes. Nat Rev Genet 4: 701-709.
    • (2003) Nat Rev Genet , vol.4 , pp. 701-709
    • Hoh, J.1    Ott, J.2
  • 16
    • 16844366786 scopus 로고    scopus 로고
    • Genome-wide strategies for detecting multiple loci that influence complex diseases
    • Marchini J, Donnelly P, Cardon LR, (2005) Genome-wide strategies for detecting multiple loci that influence complex diseases. Nat Genet 37: 413-417.
    • (2005) Nat Genet , vol.37 , pp. 413-417
    • Marchini, J.1    Donnelly, P.2    Cardon, L.R.3
  • 17
    • 36448949766 scopus 로고    scopus 로고
    • Extracting three-way gene interactions from microarray data
    • Zhang J, Ji Y, Zhang L, (2007) Extracting three-way gene interactions from microarray data. Bioinformatics 23: 2903-2909.
    • (2007) Bioinformatics , vol.23 , pp. 2903-2909
    • Zhang, J.1    Ji, Y.2    Zhang, L.3
  • 18
    • 42649089797 scopus 로고    scopus 로고
    • Composite measure of linkage disequilibrium for testing interaction between unlinked loci
    • Wu X, Jin L, Xiong M, (2008) Composite measure of linkage disequilibrium for testing interaction between unlinked loci. Eur J Hum Genet 16: 644-651.
    • (2008) Eur J Hum Genet , vol.16 , pp. 644-651
    • Wu, X.1    Jin, L.2    Xiong, M.3
  • 19
    • 0003519438 scopus 로고    scopus 로고
    • Applied multiple regression/correlation analysis for the behavioral sciences
    • Hillsdale, NJ, Lawrence Erlbaum Associates
    • Cohen J, Cohen P, West SG, Aiken LS, (2003) Applied multiple regression/correlation analysis for the behavioral sciences. Hillsdale, NJ Lawrence Erlbaum Associates.
    • (2003)
    • Cohen, J.1    Cohen, P.2    West, S.G.3    Aiken, L.S.4
  • 20
    • 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. Journal of the Royal Statistical Society, Series B 57: 289-300.
    • (1995) Journal of the Royal Statistical Society, Series B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 22
    • 52649121428 scopus 로고    scopus 로고
    • Testing gene set enrichment for subset of genes: Sub-GSE
    • Yan X, Sun F, (2008) Testing gene set enrichment for subset of genes: Sub-GSE. BMC Bioinformatics 9: 362.
    • (2008) BMC Bioinformatics , vol.9 , pp. 362
    • Yan, X.1    Sun, F.2
  • 23
    • 0029980043 scopus 로고    scopus 로고
    • p53 in growth control and neoplasia
    • Gottlieb TM, Oren M, (1996) p53 in growth control and neoplasia. Biochim Biophys Acta 1287: 77-102.
    • (1996) Biochim Biophys Acta , vol.1287 , pp. 77-102
    • Gottlieb, T.M.1    Oren, M.2
  • 24
    • 0030941458 scopus 로고    scopus 로고
    • p53, the cellular gatekeeper for growth and division
    • Levine AJ, (1997) p53, the cellular gatekeeper for growth and division. Cell 88: 323-331.
    • (1997) Cell , vol.88 , pp. 323-331
    • Levine, A.J.1
  • 25
    • 37849012181 scopus 로고    scopus 로고
    • Redox regulation of the VEGF signaling path and tissue vascularization: Hydrogen peroxide, the common link between physical exercise and cutaneous wound healing
    • Roy S, Khannaa S, Sena CK, (2008) Redox regulation of the VEGF signaling path and tissue vascularization: Hydrogen peroxide, the common link between physical exercise and cutaneous wound healing. Free Radical Biology and Medicine 44: 180-192.
    • (2008) Free Radical Biology and Medicine , vol.44 , pp. 180-192
    • Roy, S.1    Khannaa, S.2    Sena, C.K.3
  • 26
    • 31044448178 scopus 로고    scopus 로고
    • Mutant human tumor suppressor p53 modulates the activation of mitogen-activated protein kinase and nuclear factor-kappaB, but not c-Jun N-terminal kinase and activated protein-1
    • Gulati AP, Yang YM, Harter D, Mukhopadhyay A, Aggarwal BB, et al.(2006) Mutant human tumor suppressor p53 modulates the activation of mitogen-activated protein kinase and nuclear factor-kappaB, but not c-Jun N-terminal kinase and activated protein-1. Mol Carcinog 45: 26-37.
    • (2006) Mol Carcinog , vol.45 , pp. 26-37
    • Gulati, A.P.1    Yang, Y.M.2    Harter, D.3    Mukhopadhyay, A.4    Aggarwal, B.B.5
  • 27
    • 33751187663 scopus 로고    scopus 로고
    • The effects of a mutant p53 protein on the proliferation and differentiation of PC12 rat phaeochromocytoma cells
    • Fabian Z, Vecsernyes M, Pap M, Szeberenyi J, (2006) The effects of a mutant p53 protein on the proliferation and differentiation of PC12 rat phaeochromocytoma cells. J Cell Biochem 99: 1431-1441.
    • (2006) J Cell Biochem , vol.99 , pp. 1431-1441
    • Fabian, Z.1    Vecsernyes, M.2    Pap, M.3    Szeberenyi, J.4
  • 28
    • 40849124009 scopus 로고    scopus 로고
    • DNA methylation markers and early recurrence in stage I lung cancer
    • Brock MV, Hooker CM, Ota-Machida E, Han Y, Guo M, et al.(2008) DNA methylation markers and early recurrence in stage I lung cancer. N Engl J Med 358: 1118-1128.
    • (2008) N Engl J Med , vol.358 , pp. 1118-1128
    • Brock, M.V.1    Hooker, C.M.2    Ota-Machida, E.3    Han, Y.4    Guo, M.5
  • 30
    • 63449107173 scopus 로고    scopus 로고
    • A general modular framework for gene set enrichment analysis
    • Ackermann M, Strimmer K, (2009) A general modular framework for gene set enrichment analysis. BMC Bioinformatics 10: 47.
    • (2009) BMC Bioinformatics , vol.10 , pp. 47
    • Ackermann, M.1    Strimmer, K.2
  • 31
    • 0141993704 scopus 로고    scopus 로고
    • A gene-coexpression network for global discovery of conserved genetic modules
    • Stuart JM, Segal E, Koller D, Kim SK, (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302: 249-255.
    • (2003) Science , vol.302 , pp. 249-255
    • Stuart, J.M.1    Segal, E.2    Koller, D.3    Kim, S.K.4
  • 32
    • 0142045636 scopus 로고    scopus 로고
    • DNA microarray data and contextual analysis of correlation graphs
    • Rougemont J, Hingamp P, (2003) DNA microarray data and contextual analysis of correlation graphs. BMC Bioinformatics 4: 15.
    • (2003) BMC Bioinformatics , vol.4 , pp. 15
    • Rougemont, J.1    Hingamp, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.