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Volumn 43, Issue W1, 2015, Pages W57-W64

I-cisTarget 2015 update: Generalized cis-regulatory enrichment analysis in human, mouse and fly

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EID: 84949287040     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv395     Document Type: Article
Times cited : (129)

References (42)
  • 1
    • 60849139395 scopus 로고    scopus 로고
    • GOrilla: A tool for discovery and visualization of enriched GO terms in ranked gene lists
    • Eden, E., Navon, R., Steinfeld, I., Lipson, D. and Yakhini, Z. (2009) GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics, 10, 48-54.
    • (2009) BMC Bioinformatics , vol.10 , pp. 48-54
    • Eden, E.1    Navon, R.2    Steinfeld, I.3    Lipson, D.4    Yakhini, Z.5
  • 2
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang, D.W., Sherman, B.T. and Lempicki, R.A. (2008) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc., 4, 44-57.
    • (2008) Nat. Protoc. , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 3
    • 24044440971 scopus 로고    scopus 로고
    • BiNGO: A Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks
    • Maere, S., Heymans, K. and Kuiper, M. (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks. Bioinformatics, 21, 3448-3449.
    • (2005) Bioinformatics , vol.21 , pp. 3448-3449
    • Maere, S.1    Heymans, K.2    Kuiper, M.3
  • 4
    • 84883191963 scopus 로고    scopus 로고
    • OPOSSUM-3: Advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets
    • Kwon, A.T., Arenillas, D.J., Hunt, R.W. and Wasserman, W.W. (2012) oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets. G3 (Bethesda), 2, 987-1002.
    • (2012) G3 (Bethesda) , vol.2 , pp. 987-1002
    • Kwon, A.T.1    Arenillas, D.J.2    Hunt, R.W.3    Wasserman, W.W.4
  • 5
    • 48449087825 scopus 로고    scopus 로고
    • DiRE: Identifying distant regulatory elements of co-expressed genes
    • Gotea, V. and Ovcharenko, I. (2008) DiRE: identifying distant regulatory elements of co-expressed genes. Nucleic Acids Res., 36, W133-W139.
    • (2008) Nucleic Acids Res. , vol.36 , pp. W133-W139
    • Gotea, V.1    Ovcharenko, I.2
  • 6
    • 77951874066 scopus 로고    scopus 로고
    • Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers
    • Gotea, V., Visel, A., Westlund, J.M., Nobrega, M.A., Pennacchio, L.A. and Ovcharenko, I. (2010) Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. Genome Res., 20, 565-577.
    • (2010) Genome Res. , vol.20 , pp. 565-577
    • Gotea, V.1    Visel, A.2    Westlund, J.M.3    Nobrega, M.A.4    Pennacchio, L.A.5    Ovcharenko, I.6
  • 7
    • 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
  • 10
    • 79958117256 scopus 로고    scopus 로고
    • MEME-ChIP: Motif analysis of large DNA datasets
    • Machanick, P. and Bailey, T.L. (2011) MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics, 27, 1696-1697.
    • (2011) Bioinformatics , vol.27 , pp. 1696-1697
    • Machanick, P.1    Bailey, T.L.2
  • 12
    • 84880569366 scopus 로고    scopus 로고
    • Relating genes to function: Identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool
    • Auerbach, R.K., Chen, B. and Butte, A.J. (2013) Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool. Bioinformatics, 29, 1922-1924.
    • (2013) Bioinformatics , vol.29 , pp. 1922-1924
    • Auerbach, R.K.1    Chen, B.2    Butte, A.J.3
  • 15
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE Project Consortium. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
    • (2012) Nature , vol.489 , pp. 57-74
  • 16
    • 77950652940 scopus 로고    scopus 로고
    • Integrating multiple evidence sources to predict transcription factor binding in the human genome
    • Ernst, J., Plasterer, H.L., Simon, I. and Bar-Joseph, Z. (2010) Integrating multiple evidence sources to predict transcription factor binding in the human genome. Genome Res., 20, 526-536.
    • (2010) Genome Res. , vol.20 , pp. 526-536
    • Ernst, J.1    Plasterer, H.L.2    Simon, I.3    Bar-Joseph, Z.4
  • 17
    • 33644861212 scopus 로고    scopus 로고
    • ORegAnno: An open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation
    • Montgomery, S.B., Griffith, O.L., Sleumer, M.C., Bergman, C.M., Bilenky, M., Pleasance, E.D., Prychyna, Y., Zhang, X. and Jones, S.J.M. (2006) ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics, 22, 637-640.
    • (2006) Bioinformatics , vol.22 , pp. 637-640
    • Montgomery, S.B.1    Griffith, O.L.2    Sleumer, M.C.3    Bergman, C.M.4    Bilenky, M.5    Pleasance, E.D.6    Prychyna, Y.7    Zhang, X.8    Jones, S.J.M.9
  • 21
    • 84876541696 scopus 로고    scopus 로고
    • UCNEbase-A database of ultraconserved non-coding elements and genomic regulatory blocks
    • Dimitrieva, S. and Bucher, P. (2013) UCNEbase-a database of ultraconserved non-coding elements and genomic regulatory blocks. Nucleic Acids Res., 41, D101-D109.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D101-D109
    • Dimitrieva, S.1    Bucher, P.2
  • 24
    • 84867313376 scopus 로고    scopus 로고
    • I-cisTarget: An integrative genomics method for the prediction of regulatory features and cis-regulatory modules
    • Herrmann, C., de Sande, B.V., Potier, D. and Aerts, S. (2012) i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules. Nucleic Acids Res., 40, e114.
    • (2012) Nucleic Acids Res. , vol.40 , pp. e114
    • Herrmann, C.1    De Sande, B.V.2    Potier, D.3    Aerts, S.4
  • 25
    • 0042121118 scopus 로고    scopus 로고
    • Cluster-Buster: Finding dense clusters of motifs in DNA sequences
    • Frith, M.C., Li, M.C. and Weng, Z. (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    Li, M.C.2    Weng, Z.3
  • 27
    • 0141993704 scopus 로고    scopus 로고
    • A gene-coexpression network for global discovery of conserved genetic modules
    • Stuart, J.M., Segal, E., Koller, D. and Kim, S.K. (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science, 302, 249-255.
    • (2003) Science , vol.302 , pp. 249-255
    • Stuart, J.M.1    Segal, E.2    Koller, D.3    Kim, S.K.4
  • 29
    • 84882738244 scopus 로고    scopus 로고
    • Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites
    • Yan, J., Enge, M., Whitington, T., Dave, K., Liu, J., Sur, I., Schmierer, B., Jolma, A., Kivioja, T., Taipale, M. et al. (2013) Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites. Cell, 154, 801-813.
    • (2013) Cell , vol.154 , pp. 801-813
    • Yan, J.1    Enge, M.2    Whitington, T.3    Dave, K.4    Liu, J.5    Sur, I.6    Schmierer, B.7    Jolma, A.8    Kivioja, T.9    Taipale, M.10
  • 33
    • 34047192976 scopus 로고    scopus 로고
    • DNA familial binding profiles made easy: Comparison of various motif alignment and clustering strategies
    • Mahony, S., Auron, P.E. and Benos, P.V. (2007) DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies. PLoS Comput. Biol., 3, e61.
    • (2007) PLoS Comput. Biol. , vol.3 , pp. e61
    • Mahony, S.1    Auron, P.E.2    Benos, P.V.3
  • 34
    • 79551587720 scopus 로고    scopus 로고
    • Cytoscape 2.8: New features for data integration and network visualization
    • Smoot, M.E., Ono, K., Ruscheinski, J., Wang, P.-L. and Ideker, T. (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics, 27, 431-432.
    • (2011) Bioinformatics , vol.27 , pp. 431-432
    • Smoot, M.E.1    Ono, K.2    Ruscheinski, J.3    Wang, P.-L.4    Ideker, T.5
  • 36
    • 0032846542 scopus 로고    scopus 로고
    • Fusion genes in solid tumors
    • Aman, P. (1999) Fusion genes in solid tumors. Semin. Cancer Biol., 9, 303-318.
    • (1999) Semin. Cancer Biol. , vol.9 , pp. 303-318
    • Aman, P.1
  • 38
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan, A.R. and Hall, I.M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841-842.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 39
    • 84924629414 scopus 로고    scopus 로고
    • Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
    • Love, M.I., Huber, W. and Anders, S. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol., 15, 550-570.
    • (2014) Genome Biol. , vol.15 , pp. 550-570
    • Love, M.I.1    Huber, W.2    Anders, S.3
  • 40
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R. and Salzberg, S.L. (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol., 14, R36-R48.
    • (2013) Genome Biol. , vol.14 , pp. R36-R48
    • Kim, D.1    Pertea, G.2    Trapnell, C.3    Pimentel, H.4    Kelley, R.5    Salzberg, S.L.6
  • 41
    • 84928987900 scopus 로고    scopus 로고
    • HTSeq-A Python framework to work with high-throughput sequencing data
    • Anders, S., Pyl, P.T. and Huber, W. (2015) HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics, 31, 166-169.
    • (2015) Bioinformatics , vol.31 , pp. 166-169
    • Anders, S.1    Pyl, P.T.2    Huber, W.3


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