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Volumn 27, Issue 21, 2011, Pages 2972-2978

Correlated evolution of transcription factors and their binding sites

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA;

EID: 80054901781     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr503     Document Type: Article
Times cited : (22)

References (35)
  • 1
    • 64549112146 scopus 로고    scopus 로고
    • Predicting the binding preference of transcription factors to individual DNA k-mers
    • Alleyne,T.M. et al. (2009) Predicting the binding preference of transcription factors to individual DNA k-mers. Bioinformatics, 25, 1012-1018.
    • (2009) Bioinformatics , vol.25 , pp. 1012-1018
    • Alleyne, T.M.1
  • 2
    • 0031008399 scopus 로고    scopus 로고
    • A natural classification of the basic helix-loophelix class of transcription factors
    • Atchley,W.R. and Fitch,W.M. (1997) A natural classification of the basic helix-loophelix class of transcription factors. Proc. Natl Acad. Sci. USA, 94, 5172-5176.
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 5172-5176
    • Atchley, W.R.1    Fitch, W.M.2
  • 3
    • 0030707656 scopus 로고    scopus 로고
    • Structural plasticity in a remodeled protein-protein interface
    • Atwell,S. et al. (1997) Structural plasticity in a remodeled protein-protein interface. Science, 278, 1125-1128.
    • (1997) Science , vol.278 , pp. 1125-1128
    • Atwell, S.1
  • 4
    • 0031569798 scopus 로고    scopus 로고
    • The crystal structure of an intact human Max-DNA complex: new insights into mechanisms of transcriptional control
    • Brownlie,P. et al. (1997) The crystal structure of an intact human Max-DNA complex: new insights into mechanisms of transcriptional control. Structure, 5, 509-520.
    • (1997) Structure , vol.5 , pp. 509-520
    • Brownlie, P.1
  • 5
    • 0033305023 scopus 로고    scopus 로고
    • Basic helix-loop-helix proteins can act at the Ebox within the serum response element of the c-fos promoter to influence hormoneinduced promoter activation in Sertoli cells
    • Chaudhary,J. and Skinner,M.K. (1999) Basic helix-loop-helix proteins can act at the Ebox within the serum response element of the c-fos promoter to influence hormoneinduced promoter activation in Sertoli cells. Mol. Endocrinol., 13, 774-786.
    • (1999) Mol. Endocrinol. , vol.13 , pp. 774-786
    • Chaudhary, J.1    Skinner, M.K.2
  • 7
    • 77952862003 scopus 로고    scopus 로고
    • Mutual information is critically dependent on prior assumptions: would the correct estimate of mutual information please identify itself?
    • Fernandes,A.D. and Gloor,G.B. (2010) Mutual information is critically dependent on prior assumptions: would the correct estimate of mutual information please identify itself?. Bioinformatics, 26, 1135-1139.
    • (2010) Bioinformatics , vol.26 , pp. 1135-1139
    • Fernandes, A.D.1    Gloor, G.B.2
  • 8
    • 0027979220 scopus 로고
    • Structure and function of the b/HLH/Z domain of USF
    • Ferre-D'Amare,A.R. et al. (1994) Structure and function of the b/HLH/Z domain of USF. EMBO J, 13, 180-189.
    • (1994) EMBO J , vol.13 , pp. 180-189
    • Ferre-D'Amare, A.R.1
  • 9
    • 0034595516 scopus 로고    scopus 로고
    • Co-evolution of proteins with their interaction partners
    • Goh,C.S. et al. (2000) Co-evolution of proteins with their interaction partners. J. Mol. Biol., 299, 283-293.
    • (2000) J. Mol. Biol. , vol.299 , pp. 283-293
    • Goh, C.S.1
  • 10
    • 67650594823 scopus 로고    scopus 로고
    • A multiparameter network reveals extensive divergence between C. elegans bhlh transcription factors
    • Grove,C.A. et al. (2009) A multiparameter network reveals extensive divergence between C. elegans bhlh transcription factors. Cell, 138, 314-327.
    • (2009) Cell , vol.138 , pp. 314-327
    • Grove, C.A.1
  • 11
    • 44349109637 scopus 로고    scopus 로고
    • Eukaryotic transcription factor binding sites-modeling and integrative search methods
    • Hannenhalli,S. (2008) Eukaryotic transcription factor binding sites-modeling and integrative search methods. Bioinformatics, 24, 1325-1331.
    • (2008) Bioinformatics , vol.24 , pp. 1325-1331
    • Hannenhalli, S.1
  • 12
    • 67649986228 scopus 로고    scopus 로고
    • Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism
    • Huang,N. et al. (2009) Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism. Structure, 17, 939-951.
    • (2009) Structure , vol.17 , pp. 939-951
    • Huang, N.1
  • 13
    • 33747860890 scopus 로고    scopus 로고
    • TSEMA: interactive prediction of protein pairings between interacting families
    • Izarzugaza,J.M.G. et al. (2006) TSEMA: interactive prediction of protein pairings between interacting families. Nucleic Acids Res., 34, W315-W319.
    • (2006) Nucleic Acids Res. , vol.34
    • Izarzugaza, J.M.G.1
  • 14
    • 4043141372 scopus 로고    scopus 로고
    • An overview of the basic helix-loop-helix proteins
    • Jones,S. (2004) An overview of the basic helix-loop-helix proteins. Genome Biol., 5, 226.
    • (2004) Genome Biol. , vol.5 , pp. 226
    • Jones, S.1
  • 15
    • 44649193565 scopus 로고    scopus 로고
    • The RNA polymerase II core promoter - the gateway to transcription
    • Juven-Gershon,T. et al. (2008) The RNA polymerase II core promoter - the gateway to transcription, Curr. Opin. Cell Biol., 20, 253-259.
    • (2008) Curr. Opin. Cell Biol. , vol.20 , pp. 253-259
    • Juven-Gershon, T.1
  • 16
    • 18744421788 scopus 로고    scopus 로고
    • Phylogenetic analysis of the human basic helix-loop-helix proteins
    • RESEARCH0030
    • Ledent,V. et al. (2002) Phylogenetic analysis of the human basic helix-loop-helix proteins. Genome Biol., 3, RESEARCH0030.
    • (2002) Genome Biol. , vol.3
    • Ledent, V.1
  • 17
    • 78149251209 scopus 로고    scopus 로고
    • FastPval: a fast and memory efficient program to calculate very low P-values from empirical distribution
    • Li,M.J. et al. (2010) FastPval: a fast and memory efficient program to calculate very low P-values from empirical distribution. Bioinformatics, 26, 2897-2899.
    • (2010) Bioinformatics , vol.26 , pp. 2897-2899
    • Li, M.J.1
  • 18
    • 0028215362 scopus 로고
    • Crystal structure of MyoD bHLH domain-DNA complex: perspectives on DNA recognition and implications for transcriptional activation
    • Ma,P.C. et al. (1994) Crystal structure of MyoD bHLH domain-DNA complex: perspectives on DNA recognition and implications for transcriptional activation. Cell, 77, 451-459.
    • (1994) Cell , vol.77 , pp. 451-459
    • Ma, P.C.1
  • 19
    • 0028330517 scopus 로고
    • Co-evolution of ligand-receptor pairs
    • Moyle,W.R. et al. (1994) Co-evolution of ligand-receptor pairs. Nature, 368, 251-255.
    • (1994) Nature , vol.368 , pp. 251-255
    • Moyle, W.R.1
  • 20
    • 45449111373 scopus 로고    scopus 로고
    • Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites
    • Noyes,M.B. et al. (2008) Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell, 133, 1277-1289.
    • (2008) Cell , vol.133 , pp. 1277-1289
    • Noyes, M.B.1
  • 21
    • 0030821675 scopus 로고    scopus 로고
    • Correlated mutations contain information about protein-protein interaction
    • Pazos,F. et al. (1997) Correlated mutations contain information about protein-protein interaction. J. Mol. Biol., 271, 511-523.
    • (1997) J. Mol. Biol. , vol.271 , pp. 511-523
    • Pazos, F.1
  • 22
    • 0035177259 scopus 로고    scopus 로고
    • Similarity of phylogenetic trees as indicator of proteinprotein interaction
    • Pazos,F. and Valencia,A. (2001) Similarity of phylogenetic trees as indicator of proteinprotein interaction. Protein Eng., 14, 609-614.
    • (2001) Protein Eng. , vol.14 , pp. 609-614
    • Pazos, F.1    Valencia, A.2
  • 23
    • 54349091030 scopus 로고    scopus 로고
    • Protein co-evolution, co-adaptation and interactions
    • Pazos,F. and Valencia,A. (2008) Protein co-evolution, co-adaptation and interactions. EMBO J., 27, 2648-2655.
    • (2008) EMBO J. , vol.27 , pp. 2648-2655
    • Pazos, F.1    Valencia, A.2
  • 24
    • 0029789461 scopus 로고    scopus 로고
    • Searching databases of conserved sequence regions by aligning protein multiple-alignments
    • Pietrokovski,S. (1996) Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res., 24, 3836-3845.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 3836-3845
    • Pietrokovski, S.1
  • 25
    • 75549083247 scopus 로고    scopus 로고
    • JASPAR 2010: the greatly expanded openaccess database of transcription factor binding profiles
    • Portales-Casamar,E. et al. (2010) JASPAR 2010: the greatly expanded openaccess database of transcription factor binding profiles. Nucleic Acids Res., 38, D105-D110.
    • (2010) Nucleic Acids Res. , vol.38
    • Portales-Casamar, E.1
  • 26
    • 79959930131 scopus 로고    scopus 로고
    • ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor
    • Qin, J. et al. (2011) ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor. Nucleic Acids Res., 39, W430-W436.
    • (2011) Nucleic Acids Res. , vol.39
    • Qin, J.1
  • 27
    • 0030794453 scopus 로고    scopus 로고
    • Crystal structure of PHO4 bHLH domain-DNA complex: flanking base recognition
    • Shimizu,T. et al. (1997) Crystal structure of PHO4 bHLH domain-DNA complex: flanking base recognition. EMBO J., 16, 4689-4697.
    • (1997) EMBO J. , vol.16 , pp. 4689-4697
    • Shimizu, T.1
  • 28
    • 14644388890 scopus 로고    scopus 로고
    • Making connections between novel transcription factors and their DNA motifs
    • Tan,K. et al. (2005) Making connections between novel transcription factors and their DNA motifs. Genome Res., 15, 312-320.
    • (2005) Genome Res. , vol.15 , pp. 312-320
    • Tan, K.1
  • 29
    • 33646822044 scopus 로고    scopus 로고
    • Codep: maximizing co-evolutionary interdependencies to discover interacting proteins
    • Tillier,E.R.M. et al. (2006) Codep: maximizing co-evolutionary interdependencies to discover interacting proteins. Proteins, 63, 822-831.
    • (2006) Proteins , vol.63 , pp. 822-831
    • Tillier, E.R.M.1
  • 30
    • 21644454183 scopus 로고    scopus 로고
    • Scoring docking models with evolutionary information
    • Tress,M. et al. (2005) Scoring docking models with evolutionary information. Proteins, 60, 275-280.
    • (2005) Proteins , vol.60 , pp. 275-280
    • Tress, M.1
  • 31
    • 18944373328 scopus 로고    scopus 로고
    • Highly efficient endogenous human gene correction using designed zinc-finger nucleases
    • Urnov,F.D. et al. (2005) Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature, 435, 646-651.
    • (2005) Nature , vol.435 , pp. 646-651
    • Urnov, F.D.1
  • 32
    • 33745744510 scopus 로고    scopus 로고
    • Amammalian promoter model links cis elements to genetic networks
    • Wang,J.W. and Hannenhalli,S. (2006)Amammalian promoter model links cis elements to genetic networks. Biochem. Bioph. Res. Co., 347, 166-177.
    • (2006) Biochem. Bioph. Res. Co. , vol.347 , pp. 166-177
    • Wang, J.W.1    Hannenhalli, S.2
  • 33
    • 38049156077 scopus 로고    scopus 로고
    • MetaProm: a neural network based meta-predictor for alternative human promoter prediction
    • Wang,J.W. et al. (2007) MetaProm: a neural network based meta-predictor for alternative human promoter prediction. BMC Genomics, 8, 374.
    • (2007) BMC Genomics , vol.8 , pp. 374
    • Wang, J.W.1
  • 34
    • 58549114185 scopus 로고    scopus 로고
    • Identification of direct residue contacts in protein-protein interaction by message passing
    • Weigt,M. et al. (2009) Identification of direct residue contacts in protein-protein interaction by message passing. Proc. Natl Acad. Sci. USA, 106, 67-72.
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 67-72
    • Weigt, M.1
  • 35
    • 70449726432 scopus 로고    scopus 로고
    • Estimating sufficient statistics in co-evolutionary analysis by mutual information
    • Weil,P. et al. (2009) Estimating sufficient statistics in co-evolutionary analysis by mutual information. Comput. Biol. Chem., 33, 440-444.
    • (2009) Comput. Biol. Chem. , vol.33 , pp. 440-444
    • Weil, P.1


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