메뉴 건너뛰기




Volumn 45, Issue D1, 2017, Pages D643-D649

3DSNP: A database for linking human noncoding SNPs to their three-dimensional interacting genes

Author keywords

[No Author keywords available]

Indexed keywords

3DSNP DATABASE; ARTICLE; CELL INTERACTION; CHROMATIN; COMPUTER INTERFACE; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENE FREQUENCY; GENE INTERACTION; GENE LINKAGE DISEQUILIBRIUM; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC LINKAGE; GENETIC VARIABILITY; GENOTYPE; HISTONE MODIFICATION; HUMAN; PHENOTYPE; QUANTITATIVE GENETICS; QUANTITATIVE TRAIT LOCUS; SCORING SYSTEM; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGY; EPISTASIS; GENE EXPRESSION REGULATION; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; HUMAN GENOME; NUCLEIC ACID DATABASE; PROCEDURES; UNTRANSLATED REGION; WEB BROWSER;

EID: 85016086400     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw1022     Document Type: Article
Times cited : (83)

References (44)
  • 3
    • 7444260846 scopus 로고    scopus 로고
    • The ENCODE (ENCyclopedia of DNA elements) project
    • Consortium, E.P. (2004) The ENCODE (ENCyclopedia Of DNA Elements) project. Science, 306, 636-640.
    • (2004) Science , vol.306 , pp. 636-640
    • Consortium, E.P.1
  • 8
    • 84939175707 scopus 로고    scopus 로고
    • DELTA: A distal enhancer locating tool based on AdaBoost algorithm and shape features of chromatin modifications
    • Lu, Y., Qu, W., Shan, G. and Zhang, C. (2015) DELTA: a distal enhancer locating tool based on AdaBoost algorithm and shape features of chromatin modifications. PLoS One, 10, e0130622.
    • (2015) PLoS One , vol.10 , pp. e0130622
    • Lu, Y.1    Qu, W.2    Shan, G.3    Zhang, C.4
  • 10
    • 84865800494 scopus 로고    scopus 로고
    • The long-range interaction landscape of gene promoters
    • Sanyal, A., Lajoie, B.R., Jain, G. and Dekker, J. (2012) The long-range interaction landscape of gene promoters. Nature, 489, 109-113.
    • (2012) Nature , vol.489 , pp. 109-113
    • Sanyal, A.1    Lajoie, B.R.2    Jain, G.3    Dekker, J.4
  • 13
    • 84861095603 scopus 로고    scopus 로고
    • Topological domains in mammalian genomes identified by analysis of chromatin interactions
    • Dixon, J.R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J.S. and Ren, B. (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485, 376-380.
    • (2012) Nature , vol.485 , pp. 376-380
    • Dixon, J.R.1    Selvaraj, S.2    Yue, F.3    Kim, A.4    Li, Y.5    Shen, Y.6    Hu, M.7    Liu, J.S.8    Ren, B.9
  • 14
    • 66149167455 scopus 로고    scopus 로고
    • ChIP-based methods for the identification of long-range chromatin interactions
    • Fullwood, M.J. and Ruan, Y. (2009) ChIP-based methods for the identification of long-range chromatin interactions. J. Cell. Biochem., 107, 30-39.
    • (2009) J. Cell. Biochem. , vol.107 , pp. 30-39
    • Fullwood, M.J.1    Ruan, Y.2
  • 15
    • 63849091245 scopus 로고    scopus 로고
    • Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
    • Fullwood, M.J., Wei, C.L., Liu, E.T. and Ruan, Y. (2009) Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res., 19, 521-532.
    • (2009) Genome Res. , vol.19 , pp. 521-532
    • Fullwood, M.J.1    Wei, C.L.2    Liu, E.T.3    Ruan, Y.4
  • 18
    • 84939246295 scopus 로고    scopus 로고
    • CRISPR inversion of CTCF sites alters genome topology and enhancer/promoter function
    • Guo, Y., Xu, Q., Canzio, D., Shou, J., Li, J., Gorkin, D.U., Jung, I., Wu, H., Zhai, Y., Tang, Y. et al. (2015) CRISPR inversion of CTCF sites alters genome topology and enhancer/promoter function. Cell, 162, 900-910.
    • (2015) Cell , vol.162 , pp. 900-910
    • Guo, Y.1    Xu, Q.2    Canzio, D.3    Shou, J.4    Li, J.5    Gorkin, D.U.6    Jung, I.7    Wu, H.8    Zhai, Y.9    Tang, Y.10
  • 19
    • 84982859388 scopus 로고    scopus 로고
    • Defining the multivalent functions of CTCF from chromatin state and three-dimensional chromatin interactions
    • Lu, Y., Shan, G., Xue, J., Chen, C. and Zhang, C. (2016) Defining the multivalent functions of CTCF from chromatin state and three-dimensional chromatin interactions. Nucleic Acids Res., 44, 6200-6212.
    • (2016) Nucleic Acids Res. , vol.44 , pp. 6200-6212
    • Lu, Y.1    Shan, G.2    Xue, J.3    Chen, C.4    Zhang, C.5
  • 21
    • 84857707318 scopus 로고    scopus 로고
    • ChromHMM: Automating chromatin-state discovery and characterization
    • Ernst, J. and Kellis, M. (2012) ChromHMM: automating chromatin-state discovery and characterization. Nat. Methods, 9, 215-216.
    • (2012) Nat. Methods , vol.9 , pp. 215-216
    • Ernst, J.1    Kellis, M.2
  • 22
    • 84976873328 scopus 로고    scopus 로고
    • HaploReg v4: Systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease
    • Ward, L.D. and Kellis, M. (2016) HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease. Nucleic Acids Res., 44, D877-D881.
    • (2016) Nucleic Acids Res. , vol.44 , pp. D877-D881
    • Ward, L.D.1    Kellis, M.2
  • 23
    • 84858779229 scopus 로고    scopus 로고
    • HaploReg: A resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants
    • Ward, L.D. and Kellis, M. (2012) HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res., 40, D930-D934.
    • (2012) Nucleic Acids Res. , vol.40 , pp. D930-D934
    • Ward, L.D.1    Kellis, M.2
  • 24
    • 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
  • 26
    • 84970965504 scopus 로고    scopus 로고
    • CCSI: A database providing chromatin-chromatin spatial interaction information
    • Xie, X., Ma, W., Songyang, Z., Luo, Z., Huang, J., Dai, Z. and Xiong, Y. (2016) CCSI: a database providing chromatin-chromatin spatial interaction information. Database, 2016, bav124.
    • (2016) Database , vol.2016 , pp. bav124
    • Xie, X.1    Ma, W.2    Songyang, Z.3    Luo, Z.4    Huang, J.5    Dai, Z.6    Xiong, Y.7
  • 30
    • 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
  • 33
    • 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
  • 36
    • 33746078864 scopus 로고    scopus 로고
    • Large scale matching for position weight matrices
    • Liefooghe, A., Touzet, H. and Varre, J.S. (2006) Large scale matching for position weight matrices. Lect. Notes Comput. Sci., 4009, 401-412.
    • (2006) Lect. Notes Comput. Sci. , vol.4009 , pp. 401-412
    • Liefooghe, A.1    Touzet, H.2    Varre, J.S.3
  • 38
    • 84878682420 scopus 로고    scopus 로고
    • The genotype-tissue expression (GTEx) project
    • Consortium, G.T. (2013) The genotype-tissue expression (GTEx) project. Nat. Genet., 45, 580-585.
    • (2013) Nat. Genet. , vol.45 , pp. 580-585
    • Consortium, G.T.1
  • 41
    • 84940023884 scopus 로고    scopus 로고
    • Predicting the spatial organization of chromosomes using epigenetic data
    • Mourad, R. and Cuvier, O. (2015) Predicting the spatial organization of chromosomes using epigenetic data. Genome Biol., 16, 182.
    • (2015) Genome Biol. , vol.16 , pp. 182
    • Mourad, R.1    Cuvier, O.2
  • 43
    • 84976444277 scopus 로고    scopus 로고
    • De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles
    • Chen, Y., Wang, Y., Xuan, Z., Chen, M. and Zhang, M.Q. (2016) De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles. Nucleic Acids Res., 44, e106.
    • (2016) Nucleic Acids Res. , vol.44 , pp. e106
    • Chen, Y.1    Wang, Y.2    Xuan, Z.3    Chen, M.4    Zhang, M.Q.5
  • 44
    • 84940090292 scopus 로고    scopus 로고
    • Predicting chromatin organization using histone marks
    • Huang, J., Marco, E., Pinello, L. and Yuan, G.C. (2015) Predicting chromatin organization using histone marks. Genome Biol., 16, 162.
    • (2015) Genome Biol. , vol.16 , pp. 162
    • Huang, J.1    Marco, E.2    Pinello, L.3    Yuan, G.C.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.