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Volumn 30, Issue 3, 2014, Pages 360-368

Gene Sets Net Correlations Analysis (GSNCA): A multivariate differential coexpression test for gene sets

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; HUMAN; METHODOLOGY; MULTIVARIATE ANALYSIS; TUMOR CELL LINE; TUMOR SUPPRESSOR GENE;

EID: 84893275855     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt687     Document Type: Article
Times cited : (94)

References (49)
  • 1
    • 63449107173 scopus 로고    scopus 로고
    • A general modular framework for gene set enrichment analysis
    • Ackermann, M. and 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
  • 2
    • 1642317557 scopus 로고    scopus 로고
    • Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival
    • Chiaretti, S., et al. (2004) Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival. Blood, 103, 2771-2778.
    • (2004) Blood , vol.103 , pp. 2771-2778
    • Chiaretti, S.1
  • 3
    • 27144468989 scopus 로고    scopus 로고
    • Gene expression profiles of B-lineage adult acute lymphocytic leukemia reveal genetic patterns that identify lineage derivation and distinct mechanisms of transformation
    • Chiaretti, S., et al. (2005) Gene expression profiles of B-lineage adult acute lymphocytic leukemia reveal genetic patterns that identify lineage derivation and distinct mechanisms of transformation. Clin. Cancer Res., 11, 7209-7219.
    • (2005) Clin. Cancer Res , vol.11 , pp. 7209-7219
    • Chiaretti, S.1
  • 4
    • 65549155929 scopus 로고    scopus 로고
    • Identifying set-wise differential co-expression in gene expression microarray data
    • Cho, S.B., et al. (2009) Identifying set-wise differential co-expression in gene expression microarray data. BMC Bioinformatics, 10, 109.
    • (2009) BMC Bioinformatics , vol.10 , pp. 109
    • Cho, S.B.1
  • 5
    • 70350682038 scopus 로고    scopus 로고
    • Statistical methods for gene set co-expression analysis
    • Choi, Y. and Kendziorski, C. (2009) Statistical methods for gene set co-expression analysis. Bioinformatics, 25, 2780-2786.
    • (2009) Bioinformatics , vol.25 , pp. 2780-2786
    • Choi, Y.1    Kendziorski, C.2
  • 6
    • 84862889045 scopus 로고    scopus 로고
    • An empirical Bayesian approach for identifying differential coexpression in high-throughput experiments
    • Dawson, J.A. and Kendziorski, C. (2012) An empirical Bayesian approach for identifying differential coexpression in high-throughput experiments. Biometrics, 68, 455-465.
    • (2012) Biometrics , vol.68 , pp. 455-465
    • Dawson, J.A.1    Kendziorski, C.2
  • 7
    • 60749090295 scopus 로고    scopus 로고
    • Gene-set analysis and reduction
    • Dinu, I., et al. (2009) Gene-set analysis and reduction. Brief. Bioinform., 10, 24-34.
    • (2009) Brief. Bioinform , vol.10 , pp. 24-34
    • Dinu, I.1
  • 8
    • 34548747580 scopus 로고    scopus 로고
    • The chronic fatigue syndrome: A comparative pathway analysis
    • Emmert-Streib, F. (2007) The chronic fatigue syndrome: a comparative pathway analysis. J. Comput. Biol., 14, 961-972.
    • (2007) J. Comput. Biol , vol.14 , pp. 961-972
    • Emmert-Streib, F.1
  • 9
    • 79958152651 scopus 로고    scopus 로고
    • Pathway analysis of expression data: Deciphering functional building blocks of complex diseases
    • Emmert-Streib, F. and Glazko, G.V. (2011) Pathway analysis of expression data: deciphering functional building blocks of complex diseases., PLoS Comput. Biol., 7, e1002053.
    • (2011) PLoS Comput Biol , vol.7
    • Emmert-Streib, F.1    Glazko, G.V.2
  • 10
    • 84859112389 scopus 로고    scopus 로고
    • Statistical inference and reverse engineering of gene regulatory networks from observational expression data
    • Emmert-Streib, F., et al. (2012) Statistical inference and reverse engineering of gene regulatory networks from observational expression data. Front. Genet., 3, 8.
    • (2012) Front. Genet , vol.3 , pp. 8
    • Emmert-Streib, F.1
  • 11
    • 33846400424 scopus 로고    scopus 로고
    • Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
    • Faith, J.J., et al. (2007) Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol., 5, e8.
    • (2007) PLoS Biol , vol.5
    • Faith, J.J.1
  • 12
    • 77951944123 scopus 로고    scopus 로고
    • A semi-parametric Bayesian model for unsupervised differential co-expression analysis
    • Freudenberg, J.M., et al. (2010) A semi-parametric Bayesian model for unsupervised differential co-expression analysis. BMC Bioinformatics, 11, 234.
    • (2010) BMC Bioinformatics , vol.11 , pp. 234
    • Freudenberg, J.M.1
  • 13
    • 0842288337 scopus 로고    scopus 로고
    • Inferring cellular networks using probabilistic graphical models
    • Friedman, N. (2004) Inferring cellular networks using probabilistic graphical models. Science, 303, 799-805.
    • (2004) Science , vol.303 , pp. 799-805
    • Friedman, N.1
  • 14
    • 0000673504 scopus 로고
    • Multivariate generalization of the Wald- Wolfowitz and Smirnov two-sample tests
    • Friedman, J. and Rafsky, L. (1979) Multivariate generalization of the Wald- Wolfowitz and Smirnov two-sample tests. Ann. Stat., 7, 697-717.
    • (1979) Ann. Stat , vol.7 , pp. 697-717
    • Friedman, J.1    Rafsky, L.2
  • 15
    • 0033707946 scopus 로고    scopus 로고
    • Using Bayesian networks to analyze expression data
    • Friedman, N., et al. (2000) Using Bayesian networks to analyze expression data. J. Comput. Biol., 7, 601-620.
    • (2000) J. Comput. Biol , vol.7 , pp. 601-620
    • Friedman, N.1
  • 16
    • 84875380606 scopus 로고    scopus 로고
    • DiffCorr: An R package to analyze and visualize differential correlations in biological networks
    • Fukushima, A. (2013) DiffCorr: an R package to analyze and visualize differential correlations in biological networks. Gene, 518, 209-214.
    • (2013) Gene , vol.518 , pp. 209-214
    • Fukushima, A.1
  • 17
    • 0036830244 scopus 로고    scopus 로고
    • Differential cytostatic and apoptotic effects of ecteinascidin- 743 in cancer cells Transcription-dependent cell cycle arrest and transcriptionindependent JNK and mitochondrial mediated apoptosis
    • Gajate, C., et al. (2002) Differential cytostatic and apoptotic effects of ecteinascidin- 743 in cancer cells. Transcription-dependent cell cycle arrest and transcriptionindependent JNK and mitochondrial mediated apoptosis. J. Biol. Chem., 277, 41580-41589.
    • (2002) J. Biol. Chem , vol.277 , pp. 41580-41589
    • Gajate, C.1
  • 18
    • 69849105388 scopus 로고    scopus 로고
    • Unite and conquer: Univariate and multivariate approaches for finding differentially expressed gene sets
    • Glazko, G.V. and Emmert-Streib, F. (2009) Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets. Bioinformatics, 25, 2348-2354.
    • (2009) Bioinformatics , vol.25 , pp. 2348-2354
    • Glazko, G.V.1    Emmert-Streib, F.2
  • 19
    • 34249663294 scopus 로고    scopus 로고
    • Analyzing gene expression data in terms of gene sets: Methodological issues
    • Goeman, J.J. and 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
  • 20
    • 84861804088 scopus 로고    scopus 로고
    • Centrality-based pathway enrichment: A systematic approach for finding significant pathways dominated by key genes
    • Gu, Z., et al. (2012) Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes. BMC Syst. Biol., 6, 56.
    • (2012) BMC Syst. Biol , vol.6 , pp. 56
    • Gu, Z.1
  • 21
    • 46249103142 scopus 로고    scopus 로고
    • Differential variability analysis of gene expression and its application to human diseases
    • Ho, J.W., et al. (2008) Differential variability analysis of gene expression and its application to human diseases. Bioinformatics, 24, i390-i398.
    • (2008) Bioinformatics , vol.24
    • Ho, J.W.1
  • 22
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
    • Huang da, W., et al. (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res., 37, 1-13.
    • (2009) Nucleic Acids Res , vol.37 , pp. 1-13
    • Huang Da, W.1
  • 23
    • 0142121516 scopus 로고    scopus 로고
    • Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    • Irizarry, R.A., et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4, 249-264.
    • (2003) Biostatistics , vol.4 , pp. 249-264
    • Irizarry, R.A.1
  • 24
    • 61849135453 scopus 로고    scopus 로고
    • Tumor suppressors and cell metabolism: A recipe for cancer growth
    • Jones, R.G. and Thompson, C.B. (2009) Tumor suppressors and cell metabolism: a recipe for cancer growth. Genes Dev., 23, 537-548.
    • (2009) Genes Dev , vol.23 , pp. 537-548
    • Jones, R.G.1    Thompson, C.B.2
  • 25
    • 79958135926 scopus 로고    scopus 로고
    • Molecular signatures database (MSigDB) 3.0
    • Liberzon, A., et al. (2011) Molecular signatures database (MSigDB) 3.0. Bioinformatics, 27, 1739-1740.
    • (2011) Bioinformatics , vol.27 , pp. 1739-1740
    • Liberzon, A.1
  • 26
    • 33847735810 scopus 로고    scopus 로고
    • Gene alterations identified by expression profiling in tumorassociated endothelial cells from invasive ovarian carcinom
    • Lu, C., et al. (2007) Gene alterations identified by expression profiling in tumorassociated endothelial cells from invasive ovarian carcinom. Cancer Res., 67, 1757-1768.
    • (2007) Cancer Res , vol.67 , pp. 1757-1768
    • Lu, C.1
  • 27
    • 33947305781 scopus 로고    scopus 로고
    • ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
    • Margolin, A.A., et al. (2006) ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics, 7 (Suppl. 1) , S7.
    • (2006) BMC Bioinformatics , vol.7 , Issue.SUPPL. 1
    • Margolin, A.A.1
  • 29
    • 36248999573 scopus 로고    scopus 로고
    • Information-theoretic inference of large transcriptional regulatory networks
    • Meyer, P.E., et al. (2007) Information-theoretic inference of large transcriptional regulatory networks. EURASIP J. Bioinform. Syst. Biol., 2007, 79879.
    • (2007) EURASIP J. Bioinform. Syst. Biol. , vol.2007 , pp. 79879
    • Meyer, P.E.1
  • 30
    • 65549126939 scopus 로고    scopus 로고
    • Gene set internal coherence in the context of functional profiling
    • Montaner, D., et al. (2009) Gene set internal coherence in the context of functional profiling. BMC Genomics, 10, 197.
    • (2009) BMC Genomics , vol.10 , pp. 197
    • Montaner, D.1
  • 31
    • 0038054341 scopus 로고    scopus 로고
    • PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
    • Mootha, V.K., 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
  • 32
    • 0036258111 scopus 로고    scopus 로고
    • The IARC TP53 database: New online mutation analysis and recommendations to users
    • Olivier, M., et al. (2002) The IARC TP53 database: new online mutation analysis and recommendations to users. Hum. Mutat., 19, 607-614.
    • (2002) Hum. Mutat , vol.19 , pp. 607-614
    • Olivier, M.1
  • 33
    • 79851510162 scopus 로고    scopus 로고
    • Enhancing biological relevance of a weighted gene co-expression network for functional module identification
    • Prom-On, S., et al. (2011) Enhancing biological relevance of a weighted gene co-expression network for functional module identification. J. Bioinform. Comput. Biol., 9, 111-129.
    • (2011) J. Bioinform. Comput. Biol , vol.9 , pp. 111-129
    • Prom-On, S.1
  • 34
    • 84870441671 scopus 로고    scopus 로고
    • Gene set analysis for self-contained tests: Complex null and specific alternative hypotheses
    • Rahmatallah, Y., et al. (2012) Gene set analysis for self-contained tests: complex null and specific alternative hypotheses. Bioinformatics, 28, 3073-3080.
    • (2012) Bioinformatics , vol.28 , pp. 3073-3080
    • Rahmatallah, Y.1
  • 35
    • 36249019789 scopus 로고    scopus 로고
    • Dialogue on reverse-engineering assessment and methods: The DREAM of high-throughput pathway inference
    • Stolovitzky, G., et al. (2007) Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference. Ann. N. Y. Acad. Sci., 1115, 1-22.
    • (2007) Ann. N. Y. Acad. Sci , vol.1115 , pp. 1-22
    • Stolovitzky, G.1
  • 36
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
    • Subramanian, A., et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA, 102, 15545-15550.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 15545-15550
    • Subramanian, A.1
  • 37
    • 77957319820 scopus 로고    scopus 로고
    • DiffCoEx: A simple and sensitive method to find differentially coexpressed gene modules
    • Tesson, B.M., et al. (2010) DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules. BMC Bioinformatics, 11, 497.
    • (2010) BMC Bioinformatics , vol.11 , pp. 497
    • Tesson, B.M.1
  • 38
    • 26444608611 scopus 로고    scopus 로고
    • Discovering statistically significant pathways in expression profiling studies
    • Tian, L., et al. (2005) Discovering statistically significant pathways in expression profiling studies. Proc. Natl Acad. Sci. USA, 102, 13544-13549.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 13544-13549
    • Tian, L.1
  • 39
    • 84862105789 scopus 로고    scopus 로고
    • Assessment method for a power analysis to identify differentially expressed pathways
    • Tripathi, S. and Emmert-Streib, F. (2012) Assessment method for a power analysis to identify differentially expressed pathways. PLoS One, 7, e37510.
    • (2012) PLoS One , vol.7
    • Tripathi, S.1    Emmert-Streib, F.2
  • 40
    • 84876544061 scopus 로고    scopus 로고
    • Ensuring the statistical soundness of competitive gene set approaches: Gene filtering and genome-scale coverage are essential
    • Tripathi, S., et al. (2013) Ensuring the statistical soundness of competitive gene set approaches: gene filtering and genome-scale coverage are essential. Nucleic Acids Res., 41, e82.
    • (2013) Nucleic Acids Res , vol.41
    • Tripathi, S.1
  • 42
    • 34547649056 scopus 로고    scopus 로고
    • CoXpress: Differential co-expression in gene expression data
    • Watson, M. (2006) CoXpress: differential co-expression in gene expression data. BMC Bioinformatics, 7, 509.
    • (2006) BMC Bioinformatics , vol.7 , pp. 509
    • Watson, M.1
  • 43
    • 84866911829 scopus 로고    scopus 로고
    • Camera: A competitive gene set test accounting for inter-gene correlation
    • Wu, D. and Smyth, G.K. (2012) Camera: a competitive gene set test accounting for inter-gene correlation. Nucleic Acids Res., 40, e133.
    • (2012) Nucleic Acids Res , vol.40
    • Wu, D.1    Smyth, G.K.2
  • 44
    • 0035755959 scopus 로고    scopus 로고
    • Minimum spanning trees for gene expression data clustering
    • Xu, Y., et al. (2001) Minimum spanning trees for gene expression data clustering. Genome Inform., 12, 24-33.
    • (2001) Genome Inform , vol.12 , pp. 24-33
    • Xu, Y.1
  • 45
    • 12444327289 scopus 로고    scopus 로고
    • Gene expression profiling reveals progesterone-mediated cell cycle and immunoregulatory roles of Hoxa-10 in the preimplantation uterus
    • Yao, M.W., et al. (2003) Gene expression profiling reveals progesterone-mediated cell cycle and immunoregulatory roles of Hoxa-10 in the preimplantation uterus. Mol. Endocrinol., 17, 610-627.
    • (2003) Mol. Endocrinol , vol.17 , pp. 610-627
    • Yao, M.W.1
  • 46
    • 0037180503 scopus 로고    scopus 로고
    • Gene expression profiling of isogenic cells with different TP53 gene dosage reveals numerous genes that are affected by TP53 dosage and identifies CSPG2 as a direct target of p53
    • Yoon, H., et al. (2002) Gene expression profiling of isogenic cells with different TP53 gene dosage reveals numerous genes that are affected by TP53 dosage and identifies CSPG2 as a direct target of p53. Proc. Natl Acad. Sci. USA, 99, 15632-15637.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 15632-15637
    • Yoon, H.1
  • 47
    • 81955161934 scopus 로고    scopus 로고
    • Capturing changes in gene expression dynamics by gene set differential coordination analysis
    • Yu, T. and Bai, Y. (2011) Capturing changes in gene expression dynamics by gene set differential coordination analysis. Genomics, 98, 469-477.
    • (2011) Genomics , vol.98 , pp. 469-477
    • Yu, T.1    Bai, Y.2
  • 48
    • 79960892858 scopus 로고    scopus 로고
    • Link-based quantitative methods to identify differentially coexpressed genes and gene pairs
    • Yu, H., et al. (2011) Link-based quantitative methods to identify differentially coexpressed genes and gene pairs. BMC Bioinformatics, 12, 315.
    • (2011) BMC Bioinformatics , vol.12 , pp. 315
    • Yu, H.1
  • 49
    • 23944458138 scopus 로고    scopus 로고
    • A general framework for weighted gene coexpression network analysis
    • Article17
    • Zhang, B. and Horvath, S. (2005) A general framework for weighted gene coexpression network analysis. Stat. Appl. Genet. Mol. Biol., 4, Article17.
    • (2005) Stat. Appl. Genet. Mol. Biol , vol.4
    • Zhang, B.1    Horvath, S.2


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