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Volumn 23, Issue 21, 2007, Pages 2823-2828

OSCAR: One-class SVM for accurate recognition of cis-elements

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; HEPATOCYTE NUCLEAR FACTOR; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR GATA;

EID: 36448978247     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm473     Document Type: Article
Times cited : (19)

References (44)
  • 1
    • 0035112314 scopus 로고    scopus 로고
    • HNF-3 beta, C/EBP beta, and HNF-4 act in synergy to enhance transcription of the human apolipoprotein B gene in intestinal cells
    • Antes,T.J. and Levy-Wilson,B. (2001) HNF-3 beta, C/EBP beta, and HNF-4 act in synergy to enhance transcription of the human apolipoprotein B gene in intestinal cells. DNA Cell Biol., 20, 67-74.
    • (2001) DNA Cell Biol , vol.20 , pp. 67-74
    • Antes, T.J.1    Levy-Wilson, B.2
  • 3
    • 36448967213 scopus 로고    scopus 로고
    • Modeling dependence in protein-DBA binding sites
    • Berline, Germany
    • Barash,Y. et al. (2003) Modeling dependence in protein-DBA binding sites. In RECOMB'03. Berline, Germany.
    • (2003) RECOMB'03
    • Barash, Y.1
  • 4
    • 0037109192 scopus 로고    scopus 로고
    • Additive in protein-DNA interactions: How good an approximation is it?
    • Benos,P.V. et al. (2002) Additive in protein-DNA interactions: How good an approximation is it? Nucleic Acids Res., 30, 4442-4451.
    • (2002) Nucleic Acids Res , vol.30 , pp. 4442-4451
    • Benos, P.V.1
  • 5
    • 25144525014 scopus 로고    scopus 로고
    • Core transcriptional regulatory circuitry in human embryonic stem cells
    • Boyer,L.A. et al. (2005) Core transcriptional regulatory circuitry in human embryonic stem cells. Cell, 122, 947-956.
    • (2005) Cell , vol.122 , pp. 947-956
    • Boyer, L.A.1
  • 6
    • 36448982945 scopus 로고    scopus 로고
    • Chang,C.C. and Lin,C, 2001) LIBSVM: A library for support vector machines, accessed date: 28 November 2006 version 2.83
    • Chang,C.C. and Lin,C. (2001) LIBSVM: A library for support vector machines. http://www.csie.ntu.edu.tw/~cjlin/libsvm, accessed date: 28 November 2006 (version 2.83).
  • 7
    • 23144431724 scopus 로고    scopus 로고
    • P-Match: Transcription factor binding site search by combining patterns and weight matrices
    • Chekmenev,D.S. et al. (2005) P-Match: Transcription factor binding site search by combining patterns and weight matrices. Nucleic Acids Res., 33, W432-W437.
    • (2005) Nucleic Acids Res , vol.33
    • Chekmenev, D.S.1
  • 8
    • 0033500894 scopus 로고    scopus 로고
    • Shufflet: Shuffling sequences while conserving the k-let counts
    • Coward,E. (1999) Shufflet: Shuffling sequences while conserving the k-let counts. Bioinformatics, 15, 1058-1059.
    • (1999) Bioinformatics , vol.15 , pp. 1058-1059
    • Coward, E.1
  • 9
    • 0030590358 scopus 로고    scopus 로고
    • Regulatory elements in the promoter region of the rat gene encoding the acyl-CoA-binding protein
    • Elholm,M. et al. (1996) Regulatory elements in the promoter region of the rat gene encoding the acyl-CoA-binding protein. Gene, 173, 233-238.
    • (1996) Gene , vol.173 , pp. 233-238
    • Elholm, M.1
  • 10
    • 4444362206 scopus 로고    scopus 로고
    • Clustering of DNA sequences in human promoters
    • FitzGerald,P.C. et al. (2004) Clustering of DNA sequences in human promoters. Genome Res., 14, 1562-1574.
    • (2004) Genome Res , vol.14 , pp. 1562-1574
    • FitzGerald, P.C.1
  • 11
    • 0042121118 scopus 로고    scopus 로고
    • Cluster-Buster: Finding dense clusters of motifs in DNA sequences
    • Frith,M.C. et al. (2003) Cluster-Buster: Finding dense clusters of motifs in DNA sequences. Nucleic Acids Res., 31, 3666-3668.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3666-3668
    • Frith, M.C.1
  • 12
    • 0037293145 scopus 로고    scopus 로고
    • Molecular cloning of the mouse AMY-1 gene and identification of the synergistic activation of the AMY-1 promoter by GATA-1 and Sp1
    • Furusawa,M. et al. (2003) Molecular cloning of the mouse AMY-1 gene and identification of the synergistic activation of the AMY-1 promoter by GATA-1 and Sp1. Genomics, 81, 221-233.
    • (2003) Genomics , vol.81 , pp. 221-233
    • Furusawa, M.1
  • 13
    • 0028168047 scopus 로고
    • Characterization of the distal alpha-fetoprotein enhancer, a strong, long distance, liver-specific activator
    • Groupp,E.R. et al. (1994) Characterization of the distal alpha-fetoprotein enhancer, a strong, long distance, liver-specific activator. J. Biol. Chem., 269, 22178-22218.
    • (1994) J. Biol. Chem , vol.269 , pp. 22178-22218
    • Groupp, E.R.1
  • 14
    • 0036161259 scopus 로고    scopus 로고
    • Gene selection for cancer classification using support vector machines
    • Guyon,I. et al. (2002) Gene selection for cancer classification using support vector machines. Mach. Learn., 46, 389-422.
    • (2002) Mach. Learn , vol.46 , pp. 389-422
    • Guyon, I.1
  • 15
    • 2142659368 scopus 로고    scopus 로고
    • Mutation of hepatocyte nuclear factor-1beta inhibits Pkhd1 gene expression and produces renal cysts in mice
    • Hiesberger,T. et al. (2004) Mutation of hepatocyte nuclear factor-1beta inhibits Pkhd1 gene expression and produces renal cysts in mice. J. Clin. Invest., 113, 814-825.
    • (2004) J. Clin. Invest , vol.113 , pp. 814-825
    • Hiesberger, T.1
  • 16
    • 33644789724 scopus 로고    scopus 로고
    • Integrating genomic data to predict transcription factor binding
    • Holloway,D.T. et al. (2005) Integrating genomic data to predict transcription factor binding. Genome Inform., 16, 83-94.
    • (2005) Genome Inform , vol.16 , pp. 83-94
    • Holloway, D.T.1
  • 17
    • 20744453850 scopus 로고    scopus 로고
    • A boosting approach for motif modeling using ChIP-hip data
    • Hong,P. et al. (2005) A boosting approach for motif modeling using ChIP-hip data. Bioinformatics, 21, 2636-2643.
    • (2005) Bioinformatics , vol.21 , pp. 2636-2643
    • Hong, P.1
  • 18
    • 3242693303 scopus 로고    scopus 로고
    • GATA-1 and NF-Y cooperate to mediate erythroid-specific transcription of Gfi-1B gene
    • Huang,D.Y. et al. (2004) GATA-1 and NF-Y cooperate to mediate erythroid-specific transcription of Gfi-1B gene. Nucleic Acids Res. 32, 3935-3946.
    • (2004) Nucleic Acids Res , vol.32 , pp. 3935-3946
    • Huang, D.Y.1
  • 19
    • 0034048878 scopus 로고    scopus 로고
    • A discriminative framework for detecting remote protein homologies
    • Jaakkola,T. et al. (2000) A discriminative framework for detecting remote protein homologies. J. Comput. Biol., 7, 95-114.
    • (2000) J. Comput. Biol , vol.7 , pp. 95-114
    • Jaakkola, T.1
  • 20
    • 0030841937 scopus 로고    scopus 로고
    • Transcriptional regulation by glucose in the liver
    • Kahn,A. (1997) Transcriptional regulation by glucose in the liver. Biochimie, 79, 113-118.
    • (1997) Biochimie , vol.79 , pp. 113-118
    • Kahn, A.1
  • 21
    • 0041853625 scopus 로고    scopus 로고
    • ™: A tool for searching transcription factor binding sites in DNA sequences
    • ™: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res., 31, 3576-3579.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3576-3579
    • Kel, A.E.1
  • 22
    • 0030848766 scopus 로고    scopus 로고
    • Modulation of hepatic gene expression by hepatocyte nuclear factor 1
    • Ktistaki,E. and Talianidis,I. (1997) Modulation of hepatic gene expression by hepatocyte nuclear factor 1. Science, 277, 109-112.
    • (1997) Science , vol.277 , pp. 109-112
    • Ktistaki, E.1    Talianidis, I.2
  • 24
    • 1542714925 scopus 로고    scopus 로고
    • Mismatch string kernels for discriminative protein classification
    • Leslie,C.S. et al. (2004) Mismatch string kernels for discriminative protein classification. Bioinformatics, 20, 467-476.
    • (2004) Bioinformatics , vol.20 , pp. 467-476
    • Leslie, C.S.1
  • 25
    • 0035228215 scopus 로고    scopus 로고
    • BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
    • Altman,R.B, ed, Word Scientific Publish Company, Hawaii, USA, pp
    • Lin,X. et al. (2001) BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. In Altman,R.B. (ed.) Proceedings of the 6th Pacific Symposium on Biocomputing. Word Scientific Publish Company, Hawaii, USA, pp. 127-138.
    • (2001) Proceedings of the 6th Pacific Symposium on Biocomputing , pp. 127-138
    • Lin, X.1
  • 26
    • 33745456986 scopus 로고    scopus 로고
    • Odom,D.T. et al. (2006) Core transcriptional regulatory circuitry in human hepatocytes. Mol. Syst. Biol., 2, 20060017. doi:10.1038/msb4100059.
    • Odom,D.T. et al. (2006) Core transcriptional regulatory circuitry in human hepatocytes. Mol. Syst. Biol., 2, 20060017. doi:10.1038/msb4100059.
  • 27
    • 0036668278 scopus 로고    scopus 로고
    • The GATA family (vertebrates and invertebrates)
    • Patient,R.K. and Mcghee,J.D. (2002) The GATA family (vertebrates and invertebrates). Curr. Opin. Genet. Dev., 12, 416-422.
    • (2002) Curr. Opin. Genet. Dev , vol.12 , pp. 416-422
    • Patient, R.K.1    Mcghee, J.D.2
  • 28
    • 0036089483 scopus 로고    scopus 로고
    • The Eukaryotic Promoter Database, EPD: New entry types and links to gene expression data
    • Praz,V. et al. (2002) The Eukaryotic Promoter Database, EPD: New entry types and links to gene expression data. Nucleic Acids Res., 30, 322-324.
    • (2002) Nucleic Acids Res , vol.30 , pp. 322-324
    • Praz, V.1
  • 29
    • 0028971143 scopus 로고
    • MatInd and MatInspector: New fast and versatile tools for detection of consensus matches in nucleotide sequence data
    • Quandt,K. et al. (1995) MatInd and MatInspector: New fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res., 23, 4878-4884.
    • (1995) Nucleic Acids Res , vol.23 , pp. 4878-4884
    • Quandt, K.1
  • 30
    • 29144512262 scopus 로고    scopus 로고
    • RASE: Recognition of alternatively spliced exons in C.elegans
    • Ritsch,G. et al. (2005) RASE: Recognition of alternatively spliced exons in C.elegans. Bioinformatics, 21, i369-i377.
    • (2005) Bioinformatics , vol.21
    • Ritsch, G.1
  • 31
    • 33747500567 scopus 로고    scopus 로고
    • A genomic code for nucleosome positioning
    • Segal,E. et al. (2006) A genomic code for nucleosome positioning. Nature, 442, 772-778.
    • (2006) Nature , vol.442 , pp. 772-778
    • Segal, E.1
  • 32
    • 0347125328 scopus 로고    scopus 로고
    • JASPAR: An open-access database for eukaryotic transcription factor binding profiles
    • Sandelin,A. et al. (2004) JASPAR: An open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 32, 91-94.
    • (2004) Nucleic Acids Res , vol.32 , pp. 91-94
    • Sandelin, A.1
  • 33
    • 0000487102 scopus 로고    scopus 로고
    • Estimating the support of a high-dimensional distribution
    • Scholkopf,B. et al. (2001) Estimating the support of a high-dimensional distribution. Neural Comput., 13, 1443-1471.
    • (2001) Neural Comput , vol.13 , pp. 1443-1471
    • Scholkopf, B.1
  • 34
    • 29144503056 scopus 로고    scopus 로고
    • A motif-based framework for recognizing sequence families
    • Sharan,R. and Myers,E.W. (2005) A motif-based framework for recognizing sequence families. Bioinformatics, 21, i387-i393.
    • (2005) Bioinformatics , vol.21
    • Sharan, R.1    Myers, E.W.2
  • 35
    • 0037115891 scopus 로고    scopus 로고
    • Discovery of novel transcription factor binding sites by statistical overrepresentation
    • Sinha,S. and Tompa,M. (2002) Discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res. 30, 5549-5560.
    • (2002) Nucleic Acids Res , vol.30 , pp. 5549-5560
    • Sinha, S.1    Tompa, M.2
  • 37
    • 26444467746 scopus 로고    scopus 로고
    • Learning interpretable SVMs for biological sequence classification
    • Sonnenburg,S. et al. (2005b) Learning interpretable SVMs for biological sequence classification. RECOMB 2005, LNBI 3500, pp. 389-407.
    • (2005) RECOMB , vol.LNBI 3500 , pp. 389-407
    • Sonnenburg, S.1
  • 38
    • 0020480251 scopus 로고
    • Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E.coli
    • Stormo,G.D. et al. (1982) Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E.coli. Nucleic Acids Res., 10, 2997-3011.
    • (1982) Nucleic Acids Res , vol.10 , pp. 2997-3011
    • Stormo, G.D.1
  • 39
    • 77951180758 scopus 로고    scopus 로고
    • Using feature selection filtering methods for binding site prediction
    • IEEE CS Press, Beijing, China, pp
    • Sun,Y. et al. (2006) Using feature selection filtering methods for binding site prediction. In Proceedings of the 5th IEEE International Conference on Cognitive Informatics. IEEE CS Press, Beijing, China, pp. 566-571.
    • (2006) Proceedings of the 5th IEEE International Conference on Cognitive Informatics , pp. 566-571
    • Sun, Y.1
  • 40
    • 21144439147 scopus 로고    scopus 로고
    • Assessing computational tools for the discovery of transcription factor binding sites
    • Tompa,M. et al. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol., 23, 137-144.
    • (2005) Nat. Biotechnol , vol.23 , pp. 137-144
    • Tompa, M.1
  • 41
    • 36448954367 scopus 로고    scopus 로고
    • Kernels for gene regulatbry regions
    • Weiss, Y. et al, eds, MIT Press; Cambridge, MA, pp
    • Vert,J.P. et al. (2005) Kernels for gene regulatbry regions. In Weiss, Y. et al. (eds.), Advances in Neural Information Processing Systems 18. MIT Press; Cambridge, MA, pp. 1401-1408.
    • (2005) Advances in Neural Information Processing Systems 18 , pp. 1401-1408
    • Vert, J.P.1
  • 42
    • 0033976586 scopus 로고    scopus 로고
    • ®: An integral system for gene expression regulation
    • ®: An integral system for gene expression regulation. Nucleic Acids Res., 28, 316-319.
    • (2000) Nucleic Acids Res , vol.28 , pp. 316-319
    • Wingender, E.1
  • 43
    • 15244358503 scopus 로고    scopus 로고
    • Systematic discovery of regulatory motifs in human promoters and 30 UTRs by comparison of several mammals
    • Xie,X. et al. (2005) Systematic discovery of regulatory motifs in human promoters and 30 UTRs by comparison of several mammals. Nature 434, 338-345.
    • (2005) Nature , vol.434 , pp. 338-345
    • Xie, X.1
  • 44
    • 2342445980 scopus 로고    scopus 로고
    • Modeling within-motif dependence for transcription factor binding site predictions
    • Zhou,Q. and Liu,J.S. (2004) Modeling within-motif dependence for transcription factor binding site predictions. Bioinformatics, 20, 909-916.
    • (2004) Bioinformatics , vol.20 , pp. 909-916
    • Zhou, Q.1    Liu, J.S.2


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