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Volumn 25, Issue 13, 2009, Pages 1617-1624

Affinity Density: A novel genomic approach to the identification of transcription factor regulatory targets

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

EID: 67649170966     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp282     Document Type: Article
Times cited : (3)

References (33)
  • 1
    • 0027237596 scopus 로고
    • tinman and bagpipe: Two homeobox genes that determine cell fate in the dorsal mesoderm of Drosophila
    • Azpiazu,N. and Frasch,M. (1993) tinman and bagpipe: Two homeobox genes that determine cell fate in the dorsal mesoderm of Drosophila. Genes Dev., 7, 1325-1340.
    • (1993) Genes Dev , vol.7 , pp. 1325-1340
    • Azpiazu, N.1    Frasch, M.2
  • 2
    • 0037154273 scopus 로고    scopus 로고
    • Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome
    • Berman,B.P. et al. (2002) Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl Acad. Sci. USA 99, 757-762.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 757-762
    • Berman, B.P.1
  • 3
    • 12744263842 scopus 로고    scopus 로고
    • Computational identification of developmental enhancers: Conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura
    • Berman,B.P. et al. (2004) Computational identification of developmental enhancers: Conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol., 5, R61.1-R61.24.
    • (2004) Genome Biol , vol.5
    • Berman, B.P.1
  • 4
    • 0027282774 scopus 로고
    • The gene tinman is required for specification of the heart and visceral muscles in Drosophila
    • Bodmer,R. (1993) The gene tinman is required for specification of the heart and visceral muscles in Drosophila. Development, 118 719-729.
    • (1993) Development , vol.118 , pp. 719-729
    • Bodmer, R.1
  • 5
    • 33749645821 scopus 로고    scopus 로고
    • Computational identification of ftz/ftz-f1 downstream target genes
    • Bowler,T. et al. (2006) Computational identification of ftz/ftz-f1 downstream target genes. Dev. Biol., 299, 78-90.
    • (2006) Dev. Biol , vol.299 , pp. 78-90
    • Bowler, T.1
  • 6
    • 2342456392 scopus 로고    scopus 로고
    • The ladybird homeobox genes are essential for the specification of a subpopulation of neural cells
    • De Graeve,F. et al. (2004) The ladybird homeobox genes are essential for the specification of a subpopulation of neural cells. Dev. Biol., 270, 122-134.
    • (2004) Dev. Biol , vol.270 , pp. 122-134
    • De Graeve, F.1
  • 7
    • 0037100636 scopus 로고    scopus 로고
    • Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences
    • Frith,M.C. et al. (2002) Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. Nucleic Acids Res., 30, 3214-3224.
    • (2002) Nucleic Acids Res , vol.30 , pp. 3214-3224
    • Frith, M.C.1
  • 8
    • 0023239424 scopus 로고
    • Homeoboxes in the study of development
    • Gehring,W. (1987) Homeoboxes in the study of development. Science, 246, 1245-1252.
    • (1987) Science , vol.246 , pp. 1245-1252
    • Gehring, W.1
  • 9
    • 0036067977 scopus 로고    scopus 로고
    • Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model
    • Halfon,M.S. et al. (2002) Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome Res., 12, 1019-1028.
    • (2002) Genome Res , vol.12 , pp. 1019-1028
    • Halfon, M.S.1
  • 10
    • 0004181307 scopus 로고    scopus 로고
    • 3rd edn. General Publishing Company, Ltd, Toronto, Ontario
    • Hamming,R.W. (1998) Digital filters, 3rd edn. General Publishing Company, Ltd., Toronto, Ontario.
    • (1998) Digital filters
    • Hamming, R.W.1
  • 11
    • 0030840326 scopus 로고    scopus 로고
    • ladybird, a new component of the cardiogenic pathway in Drosophila required for diversification of heart precursors
    • Jagla,K. et al. (1997) ladybird, a new component of the cardiogenic pathway in Drosophila required for diversification of heart precursors. Development, 124, 3471-3479.
    • (1997) Development , vol.124 , pp. 3471-3479
    • Jagla, K.1
  • 12
    • 0036332852 scopus 로고    scopus 로고
    • Cross-repressive interactions of identity genes are essential for proper specification of cardiac and muscular fates in Drosophila
    • Jagla,T. et al. (2002) Cross-repressive interactions of identity genes are essential for proper specification of cardiac and muscular fates in Drosophila. Development, 129, 1037-1047.
    • (2002) Development , vol.129 , pp. 1037-1047
    • Jagla, T.1
  • 13
    • 33748765218 scopus 로고    scopus 로고
    • Computational biology: Toward deciphering gene regulatory information in mammalian genomes
    • Ji,H. and Wong,W.H. (2006) Computational biology: Toward deciphering gene regulatory information in mammalian genomes. Biometrics, 62, 645-663.
    • (2006) Biometrics , vol.62 , pp. 645-663
    • Ji, H.1    Wong, W.H.2
  • 14
    • 0035895925 scopus 로고    scopus 로고
    • Characterization of homo- and heterodimerization of cardiac CsxNkx2.5 homeoprotein
    • Kasahara,H. et al. (2001) Characterization of homo- and heterodimerization of cardiac CsxNkx2.5 homeoprotein. J. Biol. Chem. 276, 4570-4580.
    • (2001) J. Biol. Chem , vol.276 , pp. 4570-4580
    • Kasahara, H.1
  • 15
    • 0347719384 scopus 로고    scopus 로고
    • A functional genomic screen for cardiogenic genes by RNA interference in developing Drosophila embryos
    • Kim,Y.-O. et al. (2004) A functional genomic screen for cardiogenic genes by RNA interference in developing Drosophila embryos. Proc. Natl Acad. Sci. USA, 101, 159-164.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 159-164
    • Kim, Y.-O.1
  • 16
    • 0035477640 scopus 로고    scopus 로고
    • Molecular integration of inductive and mesodermintrinsic inputs governs even-skipped enhancer activity in a subset of pericardial and dorsal muscle progenitors
    • Knirr,S. and Frasch,M. (2001) Molecular integration of inductive and mesodermintrinsic inputs governs even-skipped enhancer activity in a subset of pericardial and dorsal muscle progenitors. Dev. Biol., 238, 13-26.
    • (2001) Dev. Biol , vol.238 , pp. 13-26
    • Knirr, S.1    Frasch, M.2
  • 17
    • 33846869288 scopus 로고    scopus 로고
    • Multiple sequence alignment: In pursuit of homologous DNA positions
    • Kumar,S. and Filipski,A. (2007) Multiple sequence alignment: In pursuit of homologous DNA positions. Genome Res., 17, 127-135.
    • (2007) Genome Res , vol.17 , pp. 127-135
    • Kumar, S.1    Filipski, A.2
  • 18
    • 0033573924 scopus 로고    scopus 로고
    • Targeted disruption of gene function in Drosophila by RNA interference (RNA-i) a role for nautilus in embryonic somatic muscle formation
    • Misquitta,L. and Paterson,B.M. (1999) Targeted disruption of gene function in Drosophila by RNA interference (RNA-i) a role for nautilus in embryonic somatic muscle formation. Proc. Natl Acad. Sci. USA, 96, 1451-1456.
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 1451-1456
    • Misquitta, L.1    Paterson, B.M.2
  • 19
    • 43349107222 scopus 로고    scopus 로고
    • A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system
    • Noyes,M.B. (2008) A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Res., 36, 2547-2560.
    • (2008) Nucleic Acids Res , vol.36 , pp. 2547-2560
    • Noyes, M.B.1
  • 20
    • 38749127589 scopus 로고    scopus 로고
    • Predicting expression patterns from regulatory sequence in Drosophila segmentation
    • Segal,E. et al. (2008) Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature, 451, 535-541.
    • (2008) Nature , vol.451 , pp. 535-541
    • Segal, E.1
  • 21
    • 0034704225 scopus 로고    scopus 로고
    • Short-range and long-range guidance by slit and its robo receptors: A combinatorial code of robo receptors controls lateral position
    • Simpson,J.H. et al. (2000) Short-range and long-range guidance by slit and its robo receptors: A combinatorial code of robo receptors controls lateral position. Cell, 103, 1019-1032.
    • (2000) Cell , vol.103 , pp. 1019-1032
    • Simpson, J.H.1
  • 22
    • 1042264827 scopus 로고    scopus 로고
    • A probabalistic method to detect regulatory modules
    • Sinha,S. et al. (2003) A probabalistic method to detect regulatory modules. Bioinformatics, 19 (Suppl. 1), i292-i301.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Sinha, S.1
  • 23
    • 0028364046 scopus 로고
    • The ventral nervous system defective gene controls proneural gene expression at two distinct steps during neuroblast formation in Drosophila
    • Skeath,J.B. et al. (1994) The ventral nervous system defective gene controls proneural gene expression at two distinct steps during neuroblast formation in Drosophila. Development, 120, 1517-1524.
    • (1994) Development , vol.120 , pp. 1517-1524
    • Skeath, J.B.1
  • 24
    • 0042121137 scopus 로고    scopus 로고
    • Target Explorer: An automated tool for the identification of new target genes for a specified set of transcription factors
    • Sosinsky,A. et al. (2003) Target Explorer: An automated tool for the identification of new target genes for a specified set of transcription factors. Nucleic Acids Res., 31, 3589-3592.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3589-3592
    • Sosinsky, A.1
  • 25
    • 5444257285 scopus 로고    scopus 로고
    • Whole-genome analysis of Drosophila gastrulation
    • Stathopoulos,A. and Levine,M. (2004) Whole-genome analysis of Drosophila gastrulation. Curr. Opin. Genet. Dev., 14, 477-484.
    • (2004) Curr. Opin. Genet. Dev , vol.14 , pp. 477-484
    • Stathopoulos, A.1    Levine, M.2
  • 26
    • 0037184519 scopus 로고    scopus 로고
    • Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo
    • Stathopoulos,A. et al. (2002) Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo. Cell, 111, 687-701.
    • (2002) Cell , vol.111 , pp. 687-701
    • Stathopoulos, A.1
  • 27
    • 61449212191 scopus 로고    scopus 로고
    • Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements
    • Taher,L. and Ovcharenko,I. (2009) Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements. Bioinformatics, 25, 578-584.
    • (2009) Bioinformatics , vol.25 , pp. 578-584
    • Taher, L.1    Ovcharenko, I.2
  • 28
    • 46249089455 scopus 로고    scopus 로고
    • Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences
    • Ward,L.D. and Bussemaker,H.J. (2008) Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. Bioinformatics, 24, i165-i171.
    • (2008) Bioinformatics , vol.24
    • Ward, L.D.1    Bussemaker, H.J.2
  • 29
    • 0034662863 scopus 로고    scopus 로고
    • Intramolecular control of transcriptional activity by the NK2-specific domain in NK-2 homeodomain proteins
    • Watada,H. et al. (2000) Intramolecular control of transcriptional activity by the NK2-specific domain in NK-2 homeodomain proteins. Proc. Natl Acad. Sci. USA, 97, 9443-9448.
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 9443-9448
    • Watada, H.1
  • 30
    • 0020787922 scopus 로고
    • Genetic and developmental analysis of the locus vnd in Drosophila melanogaster
    • White,K. et al. (1983) Genetic and developmental analysis of the locus vnd in Drosophila melanogaster. Genetics, 104, 433-448.
    • (1983) Genetics , vol.104 , pp. 433-448
    • White, K.1
  • 31
    • 0032005462 scopus 로고    scopus 로고
    • The transmembrane semaphorin Sema I is required in Drosophila for embryonic motor and CNS axon guidance
    • Yu,H.-H. et al. (1998) The transmembrane semaphorin Sema I is required in Drosophila for embryonic motor and CNS axon guidance. Neuron, 20, 207-220.
    • (1998) Neuron , vol.20 , pp. 207-220
    • Yu, H.-H.1
  • 32
    • 22144498434 scopus 로고    scopus 로고
    • The homeodomain of Tinman mediates homo- and heterodimerization of NK proteins
    • Zaffran,S. and Frasch,M. (2005) The homeodomain of Tinman mediates homo- and heterodimerization of NK proteins. Biochem. Biophys. Res. Commun. 334, 361-369.
    • (2005) Biochem. Biophys. Res. Commun , vol.334 , pp. 361-369
    • Zaffran, S.1    Frasch, M.2
  • 33
    • 0142123108 scopus 로고    scopus 로고
    • Patterning of the cardiac outflow region in Drosophila
    • Zikova,M. et al. (2003) Patterning of the cardiac outflow region in Drosophila. Proc. Natl Acad. Sci. USA, 100, 12189-12194.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 12189-12194
    • Zikova, M.1


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