메뉴 건너뛰기




Volumn 28, Issue 2, 2012, Pages 214-221

Identification of context-specific gene regulatory networks with GEMULA-gene expression modeling using LAsso

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

EID: 84856116180     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr641     Document Type: Article
Times cited : (35)

References (31)
  • 1
    • 55449128330 scopus 로고    scopus 로고
    • BATS: a Bayesian user-friendly software for analyzing time series microarray experiments
    • Angelini,C. et al. (2008) BATS: a Bayesian user-friendly software for analyzing time series microarray experiments. BMC Bioinformatics, 9:415.
    • (2008) BMC Bioinformatics , vol.9 , pp. 415
    • Angelini, C.1
  • 2
    • 33745449162 scopus 로고    scopus 로고
    • Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast
    • Balaji,S. et al. (2006) Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. J. Mol. Biol., 360, 213-227.
    • (2006) J. Mol. Biol. , vol.360 , pp. 213-227
    • Balaji, S.1
  • 3
    • 37349099750 scopus 로고    scopus 로고
    • A predictive model for transcriptional control of physiology in a free living cell
    • Bonneau,R. (2007) A predictive model for transcriptional control of physiology in a free living cell. Cell, 131, 1354-1365.
    • (2007) Cell , vol.131 , pp. 1354-1365
    • Bonneau, R.1
  • 4
    • 0035135420 scopus 로고    scopus 로고
    • Regulatory element detection using correlation with expression
    • Bussemaker,H. et al. (2001) Regulatory element detection using correlation with expression. Nat. Genet., 27, 167-171.
    • (2001) Nat. Genet. , vol.27 , pp. 167-171
    • Bussemaker, H.1
  • 5
    • 9244257298 scopus 로고    scopus 로고
    • Interacting models of cooperative gene regulation
    • Das,D. et al. (2004) Interacting models of cooperative gene regulation. Proc. Natl Acad. Sci. USA, 101, 16234-16239.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 16234-16239
    • Das, D.1
  • 6
    • 33745440791 scopus 로고    scopus 로고
    • Adaptively inferring human transcriptional subnetworks
    • Das,D. et al. (2006) Adaptively inferring human transcriptional subnetworks. Mol. Syst. Biol., 2:2006.0029.
    • (2006) Mol. Syst. Biol. , vol.2 , pp. 0029
    • Das, D.1
  • 7
    • 3242708140 scopus 로고    scopus 로고
    • Least angle regression
    • Efron,B. et al. (2004) Least angle regression. Ann. Stat., 32, 407-499.
    • (2004) Ann. Stat. , vol.32 , pp. 407-499
    • Efron, B.1
  • 8
    • 0002432565 scopus 로고
    • Multivariate adaptive regression splines
    • Friedman,J. (1991) Multivariate adaptive regression splines. Ann. Stat., 19, 1-67.
    • (1991) Ann. Stat. , vol.19 , pp. 1-67
    • Friedman, J.1
  • 9
    • 8844263909 scopus 로고    scopus 로고
    • Activated creb is sufficient to overcome inhibitors in myelin and promote spinal axon regeneration in vivo
    • Gao,Y. et al. (2004) Activated creb is sufficient to overcome inhibitors in myelin and promote spinal axon regeneration in vivo. Neuron, 44, 609-621.
    • (2004) Neuron , vol.44 , pp. 609-621
    • Gao, Y.1
  • 10
    • 0033637153 scopus 로고    scopus 로고
    • Genomic expression programs in the response of yeast cells to environmental changes
    • Gasch,A.P. et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell, 11, 4241-4257.
    • (2000) Mol. Biol. Cell , vol.11 , pp. 4241-4257
    • Gasch, A.P.1
  • 12
    • 80052214201 scopus 로고    scopus 로고
    • LLM3D: a log-linear modeling-based method to predict functional gene regulatory interactions from genome-wide expression data
    • Geeven,G. et al. (2011) LLM3D: a log-linear modeling-based method to predict functional gene regulatory interactions from genome-wide expression data. Nucleic Acids Res, 39.
    • (2011) Nucleic Acids Res , vol.39
    • Geeven, G.1
  • 13
    • 0033957693 scopus 로고    scopus 로고
    • Neurite outgrowth induced by cyclic amp can be modulated by the a subunit of go
    • Ghil,S.-H. et al. (2000) Neurite outgrowth induced by cyclic amp can be modulated by the a subunit of go. J. Neurochem., 74, 151-158.
    • (2000) J. Neurochem. , vol.74 , pp. 151-158
    • Ghil, S.-H.1
  • 14
    • 77649246145 scopus 로고    scopus 로고
    • Histone modification levels are predictive for gene expression
    • Karlić,R. et al. (2010) Histone modification levels are predictive for gene expression. Proc. Natl Acad. Sci. USA, 107, 2926-2931.
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 2926-2931
    • Karlić, R.1
  • 15
    • 73149097219 scopus 로고    scopus 로고
    • Regularized estimation of large-scale gene association networks using graphical gaussian models
    • Krämer,N. et al. (2009) Regularized estimation of large-scale gene association networks using graphical gaussian models. BMC Bioinformatics, 10, 384.
    • (2009) BMC Bioinformatics , vol.10 , pp. 384
    • Krämer, N.1
  • 16
    • 71849118200 scopus 로고    scopus 로고
    • NFIL3 and cAMP response element-binding protein form a transcriptional feedforward loop that controls neuronal regenerationassociated gene expression
    • MacGillavry,H.D. et al. (2009) NFIL3 and cAMP response element-binding protein form a transcriptional feedforward loop that controls neuronal regenerationassociated gene expression. J. Neurosci., 29, 15542-15550.
    • (2009) J. Neurosci. , vol.29 , pp. 15542-15550
    • MacGillavry, H.D.1
  • 17
    • 78751704570 scopus 로고    scopus 로고
    • Genome-wide gene expression and promoter binding analysis identifies nfil3 as a repressor of c/ebp target genes in neuronal outgrowth
    • MacGillavry,H.D. et al. (2011) Genome-wide gene expression and promoter binding analysis identifies nfil3 as a repressor of c/ebp target genes in neuronal outgrowth. Mol. Cell. Neurosci., 46, 460-468.
    • (2011) Mol. Cell. Neurosci. , vol.46 , pp. 460-468
    • MacGillavry, H.D.1
  • 18
    • 33645769260 scopus 로고    scopus 로고
    • An improved map of conserved regulatory sites for Saccharomyces cerevisiae
    • Macisaac,K. et al. (2006) An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics, 7:113.
    • (2006) BMC Bioinformatics , vol.7 , pp. 113
    • Macisaac, K.1
  • 19
    • 78651251562 scopus 로고    scopus 로고
    • Mapping dynamic histone acetylation patterns to gene expression in nanog-depleted murine embryonic stem cells
    • Markowetz,F. et al. (2010) Mapping dynamic histone acetylation patterns to gene expression in nanog-depleted murine embryonic stem cells. PLoS Comput. Biol., 6, e1001034.
    • (2010) PLoS Comput. Biol. , vol.6
    • Markowetz, F.1
  • 21
    • 78650901444 scopus 로고    scopus 로고
    • Gene regulatory networks from multifactorial perturbations using graphical lasso: application to the dream4 challenge
    • Menéndez,P. et al. (2010) Gene regulatory networks from multifactorial perturbations using graphical lasso: application to the dream4 challenge. PLoS One, 5, e14147.
    • (2010) PLoS One , vol.5 , pp. 14147
    • Menéndez, P.1
  • 22
    • 79551607002 scopus 로고    scopus 로고
    • Support union recovery in high-dimensional multivariate regression
    • Obozinski,G. et al. (2011) Support union recovery in high-dimensional multivariate regression. Ann. Stat., 39, 1-47.
    • (2011) Ann. Stat. , vol.39 , pp. 1-47
    • Obozinski, G.1
  • 23
    • 0039154020 scopus 로고
    • Neuronal traits of clonal cell lines derived by fusion of dorsal root ganglia neurons with neuroblastoma cells
    • Platika,D. et al. (1985) Neuronal traits of clonal cell lines derived by fusion of dorsal root ganglia neurons with neuroblastoma cells. Proc. Natl Acad. Sci. USA, 82, 3499-3503.
    • (1985) Proc. Natl Acad. Sci. USA , vol.82 , pp. 3499-3503
    • Platika, D.1
  • 24
    • 23944462969 scopus 로고    scopus 로고
    • Genome-wide map of nucleosome acetylation and methylation in yeast
    • Pokholok,D.K. et al. (2005) Genome-wide map of nucleosome acetylation and methylation in yeast. Cell, 122, 517-527.
    • (2005) Cell , vol.122 , pp. 517-527
    • Pokholok, D.K.1
  • 25
    • 77955868811 scopus 로고    scopus 로고
    • Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites
    • Ramsey,S.A. et al. (2010) Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites. Bioinformatics, 26, 2071-2075.
    • (2010) Bioinformatics , vol.26 , pp. 2071-2075
    • Ramsey, S.A.1
  • 26
    • 33846700587 scopus 로고    scopus 로고
    • Predicting transcription factor affinities to DNA from a biophysical model
    • Roider,H.G. et al. (2007) Predicting transcription factor affinities to DNA from a biophysical model. Bioinformatics, 23, 134-141.
    • (2007) Bioinformatics , vol.23 , pp. 134-141
    • Roider, H.G.1
  • 27
    • 84963178774 scopus 로고
    • Further analysis of the data by akaike's information criterion and the finite corrections
    • Sugiura,N. (1978) Further analysis of the data by akaike's information criterion and the finite corrections. Commun. Stat. Theor. Methods, 7, 13-26.
    • (1978) Commun. Stat. Theor. Methods , vol.7 , pp. 13-26
    • Sugiura, N.1
  • 28
    • 0001287271 scopus 로고
    • Regression shrinkage and selection via the lasso
    • Tibshirani,R. (1994) Regression shrinkage and selection via the lasso. J. R. Stat. Soc. Ser. B, 58, 267-288.
    • (1994) J. R. Stat. Soc. Ser. B , vol.58 , pp. 267-288
    • Tibshirani, R.1
  • 29
    • 55049118189 scopus 로고    scopus 로고
    • Identifying gene regulatory modules of heat shock response in yeast
    • Wu,W.S. and Li,W.H. (2008) Identifying gene regulatory modules of heat shock response in yeast. BMC Genomics, 9:439.
    • (2008) BMC Genomics , vol.9 , pp. 439
    • Wu, W.S.1    Li, W.H.2
  • 30
    • 33748753680 scopus 로고    scopus 로고
    • Statistical assessment of the global regulatory role of histone acetylation in Saccharomyces cerevisiae
    • Yuan,G.-C. et al. (2006) Statistical assessment of the global regulatory role of histone acetylation in Saccharomyces cerevisiae. Genome Biol., 7, R70.
    • (2006) Genome Biol. , vol.7 , pp. 70
    • Yuan, G.-C.1
  • 31
    • 34548536008 scopus 로고    scopus 로고
    • On the 'degrees of freedom' of the lasso
    • Zou,H. et al. (2007) On the 'degrees of freedom' of the lasso. Ann. Stat., 35, 2173-2192.
    • (2007) Ann. Stat. , vol.35 , pp. 2173-2192
    • Zou, H.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.