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Volumn 44, Issue D1, 2016, Pages D116-D125

HOCOMOCO: Expansion and enhancement of the collection of transcription factor binding sites models

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NUCLEOTIDE; TRANSCRIPTION FACTOR;

EID: 84976873260     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1249     Document Type: Article
Times cited : (166)

References (46)
  • 2
    • 84933278181 scopus 로고    scopus 로고
    • Recurrent somatic mutations in regulatory regions of human cancer genomes
    • Melton, C., Reuter, J.A., Spacek, D.V. and Snyder, M. (2015) Recurrent somatic mutations in regulatory regions of human cancer genomes. Nat. Genet., 47, 710-716.
    • (2015) Nat. Genet. , vol.47 , pp. 710-716
    • Melton, C.1    Reuter, J.A.2    Spacek, D.V.3    Snyder, M.4
  • 4
    • 84884959191 scopus 로고    scopus 로고
    • Widespread evidence of cooperative DNA binding by transcription factors in drosophila development
    • Kazemian, M., Pham, H., Wolfe, S.A., Brodsky, M.H. and Sinha, S. (2013) Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development. Nucleic Acids Res., 41, 8237-8252.
    • (2013) Nucleic Acids Res. , vol.41 , pp. 8237-8252
    • Kazemian, M.1    Pham, H.2    Wolfe, S.A.3    Brodsky, M.H.4    Sinha, S.5
  • 6
    • 84895810018 scopus 로고    scopus 로고
    • Protein-DNA binding: Complexities and multi-protein codes
    • Siggers, T. and Gordân, R. (2014) Protein-DNA binding: complexities and multi-protein codes. Nucleic Acids Res., 42, 2099-2111.
    • (2014) Nucleic Acids Res. , vol.42 , pp. 2099-2111
    • Siggers, T.1    Gordân, R.2
  • 7
    • 84879332802 scopus 로고    scopus 로고
    • DNA sequence motif: A jack of all trades for ChIP-seq data
    • Kulakovskiy, I.V. and Makeev, V.J. (2013) DNA sequence motif: a jack of all trades for ChIP-Seq data. Adv. Protein Chem. Struct. Biol., 91, 135-171.
    • (2013) Adv. Protein Chem. Struct. Biol. , vol.91 , pp. 135-171
    • Kulakovskiy, I.V.1    Makeev, V.J.2
  • 10
    • 46049087782 scopus 로고    scopus 로고
    • The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation
    • Wingender, E. (2008) The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Brief. Bioinform., 9, 326-332.
    • (2008) Brief. Bioinform. , vol.9 , pp. 326-332
    • Wingender, E.1
  • 11
    • 84876580265 scopus 로고    scopus 로고
    • SwissRegulon, a database of genome-wide annotations of regulatory sites: Recent updates
    • Pachkov, M., Balwierz, P.J., Arnold, P., Ozonov, E. and van Nimwegen, E. (2013) SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates. Nucleic Acids Res., 41, D214-D220.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D214-D220
    • Pachkov, M.1    Balwierz, P.J.2    Arnold, P.3    Ozonov, E.4    Van Nimwegen, E.5
  • 13
    • 85005773732 scopus 로고    scopus 로고
    • DNA motif databases and their uses
    • Stormo, G.D. (2015) DNA Motif Databases and Their Uses. Curr. Protoc. Bioinformatics, 51, 15.
    • (2015) Curr. Protoc. Bioinformatics , vol.51 , pp. 15
    • Stormo, G.D.1
  • 16
    • 84907536973 scopus 로고    scopus 로고
    • Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes
    • Alam, T., Medvedeva, Y.A., Jia, H., Brown, J.B., Lipovich, L. and Bajic, V.B. (2014) Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes. PLoS One, 9, e109443.
    • (2014) PLoS One , vol.9
    • Alam, T.1    Medvedeva, Y.A.2    Jia, H.3    Brown, J.B.4    Lipovich, L.5    Bajic, V.B.6
  • 18
    • 84891790072 scopus 로고    scopus 로고
    • CR cistrome: A ChIP-seq database for chromatin regulators and histone modification linkages in human and mouse
    • Wang, Q., Huang, J., Sun, H., Liu, J., Wang, J., Wang, Q., Qin, Q., Mei, S., Zhao, C., Yang, X. et al. (2014) CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse. Nucleic Acids Res., 42, D450-D458.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D450-D458
    • Wang, Q.1    Huang, J.2    Sun, H.3    Liu, J.4    Wang, J.5    Wang, Q.6    Qin, Q.7    Mei, S.8    Zhao, C.9    Yang, X.10
  • 21
    • 84983786187 scopus 로고    scopus 로고
    • Varying levels of complexity in transcription factor binding motifs
    • Keilwagen, J. and Grau, J. (2015) Varying levels of complexity in transcription factor binding motifs. Nucleic Acids Res., 43, e119.
    • (2015) Nucleic Acids Res. , vol.43 , pp. e119
    • Keilwagen, J.1    Grau, J.2
  • 22
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
    • (2009) Genome Biol. , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 23
    • 52649132425 scopus 로고    scopus 로고
    • Genome-wide identification of in vivo protein-DNA binding sites from ChIP-seq data
    • Jothi, R., Cuddapah, S., Barski, A., Cui, K. and Zhao, K. (2008) Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res., 36, 5221-5231.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 5221-5231
    • Jothi, R.1    Cuddapah, S.2    Barski, A.3    Cui, K.4    Zhao, K.5
  • 26
  • 27
    • 77952043585 scopus 로고    scopus 로고
    • Discovery of DNA motifs recognized by transcription factors through integration of different experimental sources
    • Kulakovskiy, I.V. and Makeev, V.J. (2010) Discovery of DNA motifs recognized by transcription factors through integration of different experimental sources. Biophysics (Oxford)., 54, 667-674.
    • (2010) Biophysics (Oxford) , vol.54 , pp. 667-674
    • Kulakovskiy, I.V.1    Makeev, V.J.2
  • 28
    • 84884678898 scopus 로고    scopus 로고
    • Jaccard index based similarity measure to compare transcription factor binding site models
    • Vorontsov, I.E., Kulakovskiy, I.V. and Makeev, V.J. (2013) Jaccard index based similarity measure to compare transcription factor binding site models. Algorithms Mol. Biol., 8, 23.
    • (2013) Algorithms Mol. Biol. , vol.8 , pp. 23
    • Vorontsov, I.E.1    Kulakovskiy, I.V.2    Makeev, V.J.3
  • 29
    • 77952567987 scopus 로고    scopus 로고
    • Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
    • Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y.C., Laslo, P., Cheng, J.X., Murre, C., Singh, H. and Glass, C.K. (2010) Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell, 38, 576-589.
    • (2010) Mol. Cell , vol.38 , pp. 576-589
    • Heinz, S.1    Benner, C.2    Spann, N.3    Bertolino, E.4    Lin, Y.C.5    Laslo, P.6    Cheng, J.X.7    Murre, C.8    Singh, H.9    Glass, C.K.10
  • 30
    • 84949484520 scopus 로고    scopus 로고
    • Single-cell analyses of ESCs reveal alternative pluripotent cell states and molecular mechanisms that control self-renewal
    • Papatsenko, D., Darr, H., Kulakovskiy, I.V., Waghray, A., Makeev, V.J., MacArthur, B.D. and Lemischka, I.R. (2015) Single-cell analyses of ESCs reveal alternative pluripotent cell states and molecular mechanisms that control self-renewal. Stem Cell Rep., 5, 207-220.
    • (2015) Stem Cell Rep. , vol.5 , pp. 207-220
    • Papatsenko, D.1    Darr, H.2    Kulakovskiy, I.V.3    Waghray, A.4    Makeev, V.J.5    MacArthur, B.D.6    Lemischka, I.R.7
  • 32
    • 84894573097 scopus 로고    scopus 로고
    • Large-scale quality analysis of published ChIP-seq data
    • Marinov, G.K., Kundaje, A., Park, P.J. and Wold, B.J. (2014) Large-scale quality analysis of published ChIP-seq data. G3 (Bethesda)., 4, 209-223.
    • (2014) G3 (Bethesda) , vol.4 , pp. 209-223
    • Marinov, G.K.1    Kundaje, A.2    Park, P.J.3    Wold, B.J.4
  • 33
    • 84941137652 scopus 로고    scopus 로고
    • TFClass: A classification of human transcription factors and their rodent orthologs
    • Wingender, E., Schoeps, T., Haubrock, M. and Dönitz, J. (2015) TFClass: a classification of human transcription factors and their rodent orthologs. Nucleic Acids Res., 43, D97-D102.
    • (2015) Nucleic Acids Res. , vol.43 , pp. D97-D102
    • Wingender, E.1    Schoeps, T.2    Haubrock, M.3    Dönitz, J.4
  • 34
    • 84938956077 scopus 로고    scopus 로고
    • Optimally choosing PWM motif databases and sequence scanning approaches based on ChIP-seq data
    • Dabrowski, M., Dojer, N., Krystkowiak, I., Kaminska, B. and Wilczynski, B. (2015) Optimally choosing PWM motif databases and sequence scanning approaches based on ChIP-seq data. BMC Bioinformatics, 16, 140.
    • (2015) BMC Bioinformatics , vol.16 , pp. 140
    • Dabrowski, M.1    Dojer, N.2    Krystkowiak, I.3    Kaminska, B.4    Wilczynski, B.5
  • 35
    • 39049165160 scopus 로고    scopus 로고
    • Efficient and accurate P-value computation for position weight matrices
    • Touzet, H. and Varré, J.-S. (2007) Efficient and accurate P-value computation for Position Weight Matrices. Algorithms Mol. Biol., 2, 15.
    • (2007) Algorithms Mol. Biol. , vol.2 , pp. 15
    • Touzet, H.1    Varré, J.-S.2
  • 36
    • 75949117507 scopus 로고    scopus 로고
    • MOODS: Fast search for position weight matrix matches in DNA sequences
    • Korhonen, J., Martinmäki, P., Pizzi, C., Rastas, P. and Ukkonen, E. (2009) MOODS: fast search for position weight matrix matches in DNA sequences. Bioinformatics, 25, 3181-3182.
    • (2009) Bioinformatics , vol.25 , pp. 3181-3182
    • Korhonen, J.1    Martinmäki, P.2    Pizzi, C.3    Rastas, P.4    Ukkonen, E.5
  • 37
    • 63349090507 scopus 로고    scopus 로고
    • The oncogenic EWS-FLI1 protein binds in vivo GGAA microsatellite sequences with potential transcriptional activation function
    • Guillon, N., Tirode, F., Boeva, V., Zynovyev, A., Barillot, E. and Delattre, O. (2009) The oncogenic EWS-FLI1 protein binds in vivo GGAA microsatellite sequences with potential transcriptional activation function. PLoS One, 4, e4932.
    • (2009) PLoS One , vol.4
    • Guillon, N.1    Tirode, F.2    Boeva, V.3    Zynovyev, A.4    Barillot, E.5    Delattre, O.6
  • 39
    • 84898985349 scopus 로고    scopus 로고
    • Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments
    • Kheradpour, P. and Kellis, M. (2014) Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. Nucleic Acids Res., 42, 2976-2987.
    • (2014) Nucleic Acids Res. , vol.42 , pp. 2976-2987
    • Kheradpour, P.1    Kellis, M.2
  • 41
    • 80052401846 scopus 로고    scopus 로고
    • Tree-based position weight matrix approach to model transcription factor binding site profiles
    • Bi, Y., Kim, H., Gupta, R. and Davuluri, R. V. (2011) Tree-based position weight matrix approach to model transcription factor binding site profiles. PLoS One, 6, e24210.
    • (2011) PLoS One , vol.6
    • Bi, Y.1    Kim, H.2    Gupta, R.3    Davuluri, R.V.4
  • 43
    • 84860115916 scopus 로고    scopus 로고
    • A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information
    • Ma, X., Kulkarni, A., Zhang, Z., Xuan, Z., Serfling, R. and Zhang, M.Q. (2012) A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information. Nucleic Acids Res., 40, e50.
    • (2012) Nucleic Acids Res. , vol.40 , pp. e50
    • Ma, X.1    Kulkarni, A.2    Zhang, Z.3    Xuan, Z.4    Serfling, R.5    Zhang, M.Q.6
  • 44
    • 84892758927 scopus 로고    scopus 로고
    • FootprintDB: A database of transcription factors with annotated cis elements and binding interfaces
    • Sebastian, A. and Contreras-Moreira, B. (2014) footprintDB: a database of transcription factors with annotated cis elements and binding interfaces. Bioinformatics, 30, 258-265.
    • (2014) Bioinformatics , vol.30 , pp. 258-265
    • Sebastian, A.1    Contreras-Moreira, B.2
  • 46
    • 84883488207 scopus 로고    scopus 로고
    • Yb-1 (YbX1) does not bind to Y/CCAAT boxes in vivo
    • Dolfini, D. and Mantovani, R. (2012) YB-1 (YBX1) does not bind to Y/CCAAT boxes in vivo. Oncogene, 32, 4189-4190.
    • (2012) Oncogene , vol.32 , pp. 4189-4190
    • Dolfini, D.1    Mantovani, R.2


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