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Volumn 30, Issue 7, 2014, Pages 962-970

Wigwams: Identifying gene modules co-regulated across multiple biological conditions

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARTICLE; COMPUTER PROGRAM; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; METHODOLOGY;

EID: 84897452329     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt728     Document Type: Article
Times cited : (20)

References (38)
  • 1
    • 0035367064 scopus 로고    scopus 로고
    • Whole-genome expression analysis: Challenges beyond clustering
    • Altman, R.B. and Raychaudhuri, S. (2001) Whole-genome expression analysis: challenges beyond clustering. Curr. Opin. Struct. Biol., 11, 340-347.
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 340-347
    • Altman, R.B.1    Raychaudhuri, S.2
  • 2
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology
    • Ashburner, M. et al. (2000) Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat. Genet., 25, 25-29.
    • (2000) The Gene Ontology Consortium. Nat. Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 3
    • 84878239479 scopus 로고    scopus 로고
    • Transcriptome profiling of mice testes following low dose irradiation
    • Belling, K. et al. (2013) Transcriptome profiling of mice testes following low dose irradiation. Reprod. Biol. Endocrinol., 11, 50.
    • (2013) Reprod. Biol. Endocrinol. , vol.11 , pp. 50
    • Belling, K.1
  • 4
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B Methodol., 57, 289-300.
    • (1995) J. R. Stat. Soc. B Methodol. , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 5
    • 0028931857 scopus 로고
    • Multiple significance tests: The bonferroni method
    • Bland, J.M. and Altman, D.G. (1995) Multiple significance tests: the bonferroni method. BMJ, 310, 170.
    • (1995) BMJ , vol.310 , pp. 170
    • Bland, J.M.1    Altman, D.G.2
  • 6
    • 79955626693 scopus 로고    scopus 로고
    • High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation
    • Breeze, E. et al. (2011) High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation. Plant Cell, 23, 873-894.
    • (2011) Plant Cell , vol.23 , pp. 873-894
    • Breeze, E.1
  • 7
    • 84879967750 scopus 로고    scopus 로고
    • MEME-LaB: Motif analysis in clusters
    • Brown, P. et al. (2013) MEME-LaB: motif analysis in clusters. Bioinformatics, 29, 1696-1697.
    • (2013) Bioinformatics , vol.29 , pp. 1696-1697
    • Brown, P.1
  • 8
    • 84856598466 scopus 로고    scopus 로고
    • The role of WRKY transcription factors in plant abiotic stresses
    • Chen, L. et al. (2012) The role of WRKY transcription factors in plant abiotic stresses. Biochim. Biophys. Acta, 1819, 120-128.
    • (2012) Biochim. Biophys. Acta , vol.1819 , pp. 120-128
    • Chen, L.1
  • 9
    • 0033119581 scopus 로고    scopus 로고
    • The TCP domain: A motif found in proteins regulating plant growth and development
    • Cubas, P. et al. (1999) The TCP domain: a motif found in proteins regulating plant growth and development. Plant J., 18, 215-222.
    • (1999) Plant J. , vol.18 , pp. 215-222
    • Cubas, P.1
  • 10
    • 0029803731 scopus 로고    scopus 로고
    • Characterization of a zinc-dependent transcriptional activator from Arabidopsis
    • de Pater, S. et al. (1996) Characterization of a zinc-dependent transcriptional activator from Arabidopsis. Nucleic Acids Res., 24, 4624-4631.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 4624-4631
    • De Pater, S.1
  • 12
    • 34547219390 scopus 로고    scopus 로고
    • Networks of WRKY transcription factors in defense signaling
    • Eulgem, T. and Somssich, I.E. (2007) Networks of WRKY transcription factors in defense signaling. Curr. Opin. Plant Biol., 10, 366-371.
    • (2007) Curr. Opin. Plant Biol. , vol.10 , pp. 366-371
    • Eulgem, T.1    Somssich, I.E.2
  • 13
    • 0034192491 scopus 로고    scopus 로고
    • The WRKY superfamily of plant transcription factors
    • Eulgem, T. et al. (2000) The WRKY superfamily of plant transcription factors. Trends Plant Sci., 5, 199-206.
    • (2000) Trends Plant Sci. , vol.5 , pp. 199-206
    • Eulgem, T.1
  • 14
    • 28044449342 scopus 로고    scopus 로고
    • Bayesian coclustering of Anopheles gene expression time series: Study of immune defense response to multiple experimental challenges
    • Heard, N.A. et al. (2005) Bayesian coclustering of Anopheles gene expression time series: study of immune defense response to multiple experimental challenges. Proc. Natl. Acad. Sci. USA, 102, 16939-16944.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 16939-16944
    • Heard, N.A.1
  • 15
    • 84879213336 scopus 로고    scopus 로고
    • A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves
    • Hickman, R. et al. (2013) A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves. Plant J., 75, 26-39.
    • (2013) Plant J. , vol.75 , pp. 26-39
    • Hickman, R.1
  • 16
    • 0032918558 scopus 로고    scopus 로고
    • Plant cis-acting regulatory DNA elements (PLACE) database: 1999
    • Higo, K. et al. (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res., 27, 297-300.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 297-300
    • Higo, K.1
  • 17
    • 34247200577 scopus 로고    scopus 로고
    • The AtGenExpress global stress expression data set: Protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses
    • Kilian, J. et al. (2007) The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J., 50, 347-363.
    • (2007) Plant J. , vol.50 , pp. 347-363
    • Kilian, J.1
  • 18
    • 84896484065 scopus 로고    scopus 로고
    • Inference of dynamic networks using time-course data
    • doi:10.1093/bib/bbt028
    • Kim, Y. et al. (2013) Inference of dynamic networks using time-course data. Brief. Bioinform., doi:10.1093/bib/bbt028.
    • (2013) Brief. Bioinform.
    • Kim, Y.1
  • 19
    • 84872549196 scopus 로고    scopus 로고
    • MultiFacTV: Finding modules from higher-order gene expression profiles with time dimension
    • Li, X. et al. (2012) MultiFacTV: finding modules from higher-order gene expression profiles with time dimension. In: IEEE International Conference on Bioinformatics and Biomedicine. pp. 1-6.
    • (2012) IEEE International Conference on Bioinformatics and Biomedicine , pp. 1-6
    • Li, X.1
  • 20
    • 76849109141 scopus 로고    scopus 로고
    • Identification of regulatory modules in time series gene expression data using a linear time biclustering algorithm
    • Madeira, S.C. et al. (2010) Identification of regulatory modules in time series gene expression data using a linear time biclustering algorithm. IEEE/ACM Trans. Comput. Biol. Bioinform., 7, 153-165.
    • (2010) IEEE/ACM Trans. Comput. Biol. Bioinform. , vol.7 , pp. 153-165
    • Madeira, S.C.1
  • 21
    • 24044440971 scopus 로고    scopus 로고
    • BiNGO: A Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks
    • Maere, S. et al. (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics, 21, 3448-3449.
    • (2005) Bioinformatics , vol.21 , pp. 3448-3449
    • Maere, S.1
  • 22
    • 44149121700 scopus 로고    scopus 로고
    • Extracting expression modules from perturbational gene expression compendia
    • Maere, S. et al. (2008) Extracting expression modules from perturbational gene expression compendia. BMC Syst. Biol., 2, 33.
    • (2008) BMC Syst. Biol. , vol.2 , pp. 33
    • Maere, S.1
  • 23
    • 73449098946 scopus 로고    scopus 로고
    • TCP genes: A family snapshot ten years later
    • Mart?n-Trillo, M. and Cubas, P. (2010) TCP genes: a family snapshot ten years later. Trends Plant Sci., 15, 31-39.
    • (2010) Trends Plant Sci. , vol.15 , pp. 31-39
    • Martn-Trillo, M.1    Cubas, P.2
  • 24
    • 33644876958 scopus 로고    scopus 로고
    • TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes
    • Matys, V. et al. (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res., 34, D108-D110.
    • (2006) Nucleic Acids Res. , vol.34
    • Matys, V.1
  • 25
    • 66349129690 scopus 로고    scopus 로고
    • Enrichment constrained time-dependent clustering analysis for finding meaningful temporal transcription modules
    • Meng, J. et al. (2009) Enrichment constrained time-dependent clustering analysis for finding meaningful temporal transcription modules. Bioinformatics, 25, 1521-1527.
    • (2009) Bioinformatics , vol.25 , pp. 1521-1527
    • Meng, J.1
  • 26
    • 2342501846 scopus 로고    scopus 로고
    • Development and evaluation of an Arabidopsis whole genome Affymetrix probe array
    • Redman, J.C. et al. (2004) Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. Plant J., 38, 545-561.
    • (2004) Plant J. , vol.38 , pp. 545-561
    • Redman, J.C.1
  • 27
    • 33746067911 scopus 로고    scopus 로고
    • Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks
    • Reiss, D.J. et al. (2006) Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics, 7, 280.
    • (2006) BMC Bioinformatics , vol.7 , pp. 280
    • Reiss, D.J.1
  • 28
    • 80051746279 scopus 로고    scopus 로고
    • Hormone crosstalk in plant disease and defense: More than just jasmonate-salicylate antagonism
    • Robert-Seilaniantz, A. et al. (2011) Hormone crosstalk in plant disease and defense: more than just jasmonate-salicylate antagonism. Annu. Rev. Phytopathol., 49, 317-343.
    • (2011) Annu. Rev. Phytopathol. , vol.49 , pp. 317-343
    • Robert-Seilaniantz, A.1
  • 29
    • 34547633677 scopus 로고    scopus 로고
    • Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
    • Robertson, G.G. et al. (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods, 4, 651-657.
    • (2007) Nat. Methods , vol.4 , pp. 651-657
    • Robertson, G.G.1
  • 30
    • 69849104854 scopus 로고    scopus 로고
    • R/BHC: Fast Bayesian hierarchical clustering for microarray data
    • Savage, R.S. et al. (2009) R/BHC: fast Bayesian hierarchical clustering for microarray data. BMC Bioinformatics, 10, 242.
    • (2009) BMC Bioinformatics , vol.10 , pp. 242
    • Savage, R.S.1
  • 31
    • 37249069096 scopus 로고    scopus 로고
    • CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes
    • Sclep, G. et al. (2007) CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes. BMC Bioinformatics, 8, 400.
    • (2007) BMC Bioinformatics , vol.8 , pp. 400
    • Sclep, G.1
  • 32
    • 77950803115 scopus 로고    scopus 로고
    • A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series
    • Stegle, O. et al. (2010) A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series. J. Comput. Biol., 17, 355-367.
    • (2010) J. Comput. Biol. , vol.17 , pp. 355-367
    • Stegle, O.1
  • 33
    • 35748941236 scopus 로고    scopus 로고
    • EDISA: Extracting biclusters from multiple time-series of gene expression profiles
    • Supper, J. et al. (2007) EDISA: extracting biclusters from multiple time-series of gene expression profiles. BMC Bioinformatics, 8, 334.
    • (2007) BMC Bioinformatics , vol.8 , pp. 334
    • Supper, J.1
  • 34
    • 0042930859 scopus 로고    scopus 로고
    • Genomic effects of IFN-beta in multiple sclerosis patients
    • Weinstock-Guttman, B. et al. (2003) Genomic effects of IFN-beta in multiple sclerosis patients. J. Immunol., 171, 2694-2702.
    • (2003) J. Immunol. , vol.171 , pp. 2694-2702
    • Weinstock-Guttman, B.1
  • 35
    • 33745647013 scopus 로고    scopus 로고
    • Overrepresentation of elements recognized by TCP-domain transcription factors in the upstream regions of nuclear genes encoding components of the mitochondrial oxidative phosphorylation machinery
    • Welchen, E. and Gonzalez, D.H. (2006) Overrepresentation of elements recognized by TCP-domain transcription factors in the upstream regions of nuclear genes encoding components of the mitochondrial oxidative phosphorylation machinery. Plant Physiol., 141, 540-545.
    • (2006) Plant Physiol. , vol.141 , pp. 540-545
    • Welchen, E.1    Gonzalez, D.H.2
  • 36
    • 84868288164 scopus 로고    scopus 로고
    • Arabidopsis defense against Botrytis cinerea: Chronology and regulation deciphered by high-resolution temporal transcriptomic analysis
    • Windram, O. et al. (2012) Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis. Plant Cell, 24, 3530-3557.
    • (2012) Plant Cell , vol.24 , pp. 3530-3557
    • Windram, O.1
  • 37
    • 4844229238 scopus 로고    scopus 로고
    • From co-expression to co-regulation: How many microarray experiments do we need?
    • Yeung, K.Y. et al. (2004) From co-expression to co-regulation: how many microarray experiments do we need? Genome Biol., 5, R48.
    • (2004) Genome Biol. , vol.5
    • Yeung, K.Y.1
  • 38
    • 84868708561 scopus 로고    scopus 로고
    • A unified adaptive co-identification framework for high-d expression data
    • In: Shibuya, T., Kashima, H., Sese, J. and Ahmad, S. (eds), Springer, Berlin, Heidelberg
    • Zhang, S. et al. (2012) A unified adaptive co-identification framework for high-d expression data. In: Shibuya, T., Kashima, H., Sese, J. and Ahmad, S. (eds) Lecture Notes in Computer Science. Vol. 7632, Springer, Berlin, Heidelberg, pp. 59-70.
    • (2012) Lecture Notes in Computer Science , vol.7632 , pp. 59-70
    • Zhang, S.1


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