메뉴 건너뛰기




Volumn 44, Issue D1, 2016, Pages D126-D132

ORegAnno 3.0: A community-driven resource for curated regulatory annotation

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; SMALL UNTRANSLATED RNA; TRANSCRIPTION FACTOR; RNA;

EID: 84976866487     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1203     Document Type: Article
Times cited : (134)

References (51)
  • 1
    • 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. (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.9
  • 3
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • The 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
  • 4
    • 84875847924 scopus 로고    scopus 로고
    • Is junk DNA bunk? A critique of ENCODE
    • Doolittle, W.F. (2013) Is junk DNA bunk? A critique of ENCODE. Proc. Natl. Acad. Sci. U.S.A., 110, 5294-5300.
    • (2013) Proc. Natl. Acad. Sci. U.S.A. , vol.110 , pp. 5294-5300
    • Doolittle, W.F.1
  • 5
    • 84876031068 scopus 로고    scopus 로고
    • The ENCODE project: Missteps overshadowing a success
    • Eddy, S.R. (2013) The ENCODE project: missteps overshadowing a success. Curr. Biol., 23, R259-261.
    • (2013) Curr. Biol. , vol.23 , pp. R259-R261
    • Eddy, S.R.1
  • 6
    • 84875275808 scopus 로고    scopus 로고
    • On the immortality of television sets: 'Function' in the human genome according to the evolution-free gospel of ENCODE
    • Graur, D., Zheng, Y., Price, N., Azevedo, R.B., Zufall, R.A. and Elhaik, E. (2013) On the immortality of television sets: 'function' in the human genome according to the evolution-free gospel of ENCODE. Genome Biol. Evol., 5, 578-590.
    • (2013) Genome Biol. Evol. , vol.5 , pp. 578-590
    • Graur, D.1    Zheng, Y.2    Price, N.3    Azevedo, R.B.4    Zufall, R.A.5    Elhaik, E.6
  • 10
    • 48449105268 scopus 로고    scopus 로고
    • ConTra: A promoter alignment analysis tool for identification of transcription factor binding sites across species
    • Hooghe, B., Hulpiau, P., van Roy, F. and De Bleser, P. (2008) ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species. Nucleic Acids Res., 36, W128-W132.
    • (2008) Nucleic Acids Res. , vol.36 , pp. W128-W132
    • Hooghe, B.1    Hulpiau, P.2    Van Roy, F.3    De Bleser, P.4
  • 12
    • 84949287040 scopus 로고    scopus 로고
    • I-cisTarget 2015 update: Generalized cis-regulatory enrichment analysis in human, mouse and fly
    • Imrichova, H., Hulselmans, G., Atak, Z.K., Potier, D. and Aerts, S. (2015) i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly. Nucleic Acids Res., 43, W57-W64.
    • (2015) Nucleic Acids Res. , vol.43 , pp. W57-W64
    • Imrichova, H.1    Hulselmans, G.2    Atak, Z.K.3    Potier, D.4    Aerts, S.5
  • 13
    • 84903527058 scopus 로고    scopus 로고
    • LASAGNA-search 2.0: Integrated transcription factor binding site search and visualization in a browser
    • Lee, C. and Huang, C.H. (2014) LASAGNA-Search 2.0: integrated transcription factor binding site search and visualization in a browser. Bioinformatics, 30, 1923-1925.
    • (2014) Bioinformatics , vol.30 , pp. 1923-1925
    • Lee, C.1    Huang, C.H.2
  • 15
    • 84871430267 scopus 로고    scopus 로고
    • An integrative approach to inferring gene regulatory module networks
    • Baitaluk, M., Kozhenkov, S. and Ponomarenko, J. (2012) An integrative approach to inferring gene regulatory module networks. PLoS One, 7, e52836.
    • (2012) PLoS One , vol.7
    • Baitaluk, M.1    Kozhenkov, S.2    Ponomarenko, J.3
  • 18
    • 78049437880 scopus 로고    scopus 로고
    • Use of data-biased random walks on graphs for the retrieval of context-specific networks from genomic data
    • Komurov, K., White, M.A. and Ram, P.T. (2010) Use of data-biased random walks on graphs for the retrieval of context-specific networks from genomic data. PLoS Comput. Biol., 6, e1000889.
    • (2010) PLoS Comput. Biol. , vol.6
    • Komurov, K.1    White, M.A.2    Ram, P.T.3
  • 23
    • 84883583576 scopus 로고    scopus 로고
    • GWAS3D: Detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications
    • Li, M.J., Wang, L.Y., Xia, Z., Sham, P.C. and Wang, J. (2013) GWAS3D: Detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications. Nucleic Acids Res., 41, W150-W158.
    • (2013) Nucleic Acids Res. , vol.41 , pp. W150-W158
    • Li, M.J.1    Wang, L.Y.2    Xia, Z.3    Sham, P.C.4    Wang, J.5
  • 27
    • 0141815478 scopus 로고    scopus 로고
    • Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes
    • Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W. and Haussler, D. (2003) Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl. Acad. Sci. U.S.A., 100, 11484-11489.
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , pp. 11484-11489
    • Kent, W.J.1    Baertsch, R.2    Hinrichs, A.3    Miller, W.4    Haussler, D.5
  • 28
    • 33846112470 scopus 로고    scopus 로고
    • VISTA enhancer browser - A database of tissue-specific human enhancers
    • Visel, A., Minovitsky, S., Dubchak, I. and Pennacchio, L.A. (2007) VISTA Enhancer Browser - a database of tissue-specific human enhancers. Nucleic Acids Res., 35, D88-D92.
    • (2007) Nucleic Acids Res. , vol.35 , pp. D88-D92
    • Visel, A.1    Minovitsky, S.2    Dubchak, I.3    Pennacchio, L.A.4
  • 30
    • 78651335916 scopus 로고    scopus 로고
    • REDfly v3.0: Toward a comprehensive database of transcriptional regulatory elements in drosophila
    • Gallo, S.M., Gerrard, D.T., Miner, D., Simich, M., Soye, B., Bergman, C.M. and Halfon, M.S. (2011) REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Res., 39, D118-D123.
    • (2011) Nucleic Acids Res. , vol.39 , pp. D118-D123
    • Gallo, S.M.1    Gerrard, D.T.2    Miner, D.3    Simich, M.4    Soye, B.5    Bergman, C.M.6    Halfon, M.S.7
  • 31
    • 17444402501 scopus 로고    scopus 로고
    • Drosophila DNase I footprint database: A systematic genome annotation of transcription factor binding sites in the fruitfly, drosophila melanogaster
    • Bergman, C.M., Carlson, J.W. and Celniker, S.E. (2005) Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster. Bioinformatics, 21, 1747-1749.
    • (2005) Bioinformatics , vol.21 , pp. 1747-1749
    • Bergman, C.M.1    Carlson, J.W.2    Celniker, S.E.3
  • 35
    • 77955963884 scopus 로고    scopus 로고
    • Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
    • Betel, D., Koppal, A., Agius, P., Sander, C. and Leslie, C. (2010) Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol., 11, R90.
    • (2010) Genome Biol. , vol.11 , pp. R90
    • Betel, D.1    Koppal, A.2    Agius, P.3    Sander, C.4    Leslie, C.5
  • 37
    • 84887423584 scopus 로고    scopus 로고
    • The NFI-regulome database: A tool for annotation and analysis of control regions of genes regulated by nuclear factor I transcription factors
    • Gronostajski, R.M., Guaneri, J., Lee, D.H. and Gallo, S.M. (2011) The NFI-Regulome Database: A tool for annotation and analysis of control regions of genes regulated by Nuclear Factor I transcription factors. J. Clin. Bioinforma, 1, 4.
    • (2011) J. Clin. Bioinforma , vol.1 , pp. 4
    • Gronostajski, R.M.1    Guaneri, J.2    Lee, D.H.3    Gallo, S.M.4
  • 38
    • 70350741353 scopus 로고    scopus 로고
    • Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention
    • Hufton, A.L., Mathia, S., Braun, H., Georgi, U., Lehrach, H., Vingron, M., Poustka, A.J. and Panopoulou, G. (2009) Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention. Genome Res., 19, 2036-2051.
    • (2009) Genome Res. , vol.19 , pp. 2036-2051
    • Hufton, A.L.1    Mathia, S.2    Braun, H.3    Georgi, U.4    Lehrach, H.5    Vingron, M.6    Poustka, A.J.7    Panopoulou, G.8
  • 39
    • 34547838179 scopus 로고    scopus 로고
    • Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation
    • Lim, C.A., Yao, F., Wong, J.J., George, J., Xu, H., Chiu, K.P., Sung, W.K., Lipovich, L., Vega, V.B., Chen, J. et al. (2007) Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation. Mol. Cell, 27, 622-635.
    • (2007) Mol. Cell , vol.27 , pp. 622-635
    • Lim, C.A.1    Yao, F.2    Wong, J.J.3    George, J.4    Xu, H.5    Chiu, K.P.6    Sung, W.K.7    Lipovich, L.8    Vega, V.B.9    Chen, J.10
  • 41
    • 38049007472 scopus 로고    scopus 로고
    • Genome-wide identification of estrogen receptor alpha-binding sites in mouse liver
    • Gao, H., Falt, S., Sandelin, A., Gustafsson, J.A. and Dahlman-Wright, K. (2008) Genome-wide identification of estrogen receptor alpha-binding sites in mouse liver. Mol. Endocrinol., 22, 10-22.
    • (2008) Mol. Endocrinol. , vol.22 , pp. 10-22
    • Gao, H.1    Falt, S.2    Sandelin, A.3    Gustafsson, J.A.4    Dahlman-Wright, K.5
  • 46
    • 0033568462 scopus 로고    scopus 로고
    • Telomere shortening and apoptosis in telomerase-inhibited human tumor cells
    • Zhang, X., Mar, V., Zhou, W., Harrington, L. and Robinson, M.O. (1999) Telomere shortening and apoptosis in telomerase-inhibited human tumor cells. Genes Dev., 13, 2388-2399.
    • (1999) Genes Dev. , vol.13 , pp. 2388-2399
    • Zhang, X.1    Mar, V.2    Zhou, W.3    Harrington, L.4    Robinson, M.O.5
  • 47
    • 84922527340 scopus 로고    scopus 로고
    • Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types
    • Fredriksson, N.J., Ny, L., Nilsson, J.A. and Larsson, E. (2014) Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types. Nat. Genet., 46, 1258-1263.
    • (2014) Nat. Genet. , vol.46 , pp. 1258-1263
    • Fredriksson, N.J.1    Ny, L.2    Nilsson, J.A.3    Larsson, E.4
  • 48
    • 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
  • 49
    • 84908894973 scopus 로고    scopus 로고
    • Genome-wide analysis of noncoding regulatory mutations in cancer
    • Weinhold, N., Jacobsen, A., Schultz, N., Sander, C. and Lee, W. (2014) Genome-wide analysis of noncoding regulatory mutations in cancer. Nat. Genet., 46, 1160-1165.
    • (2014) Nat. Genet. , vol.46 , pp. 1160-1165
    • Weinhold, N.1    Jacobsen, A.2    Schultz, N.3    Sander, C.4    Lee, W.5
  • 51
    • 84875634162 scopus 로고    scopus 로고
    • Integrative genomics viewer (IGV): High-performance genomics data visualization and exploration
    • Thorvaldsdottir, H., Robinson, J.T. and Mesirov, J.P. (2013) Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform., 14, 178-192.
    • (2013) Brief Bioinform. , vol.14 , pp. 178-192
    • Thorvaldsdottir, H.1    Robinson, J.T.2    Mesirov, J.P.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.