메뉴 건너뛰기




Volumn 4, Issue 3, 2016, Pages 217-225

Advances in computational ChIA-PET data analysis

Author keywords

[No Author keywords available]

Indexed keywords


EID: 85016035197     PISSN: 20954689     EISSN: 20954697     Source Type: Journal    
DOI: 10.1007/s40484-016-0080-3     Document Type: Review
Times cited : (6)

References (32)
  • 2
    • 84862908850 scopus 로고    scopus 로고
    • Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation
    • COI: 1:CAS:528:DC%2BC38XhtFKgtrY%3D, PID: 22265404
    • Li, G., Ruan, X., Auerbach, R. K., Sandhu, K. S., Zheng, M., Wang, P., Poh, H. M., Goh, Y., Lim, J., Zhang, J., et al. (2012) Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell, 148, 84–98
    • (2012) Cell , vol.148 , pp. 84-98
    • Li, G.1    Ruan, X.2    Auerbach, R.K.3    Sandhu, K.S.4    Zheng, M.5    Wang, P.6    Poh, H.M.7    Goh, Y.8    Lim, J.9    Zhang, J.10
  • 5
    • 84950235577 scopus 로고    scopus 로고
    • MICC: an R package for identifying chromatin interactions from ChIA-PET data
    • COI: 1:CAS:528:DC%2BC28Xht1CitLrM, PID: 26231426
    • He, C., Zhang, M. Q. and Wang, X. (2015) MICC: an R package for identifying chromatin interactions from ChIA-PET data. Bioinformatics, 31, 3832–3834
    • (2015) Bioinformatics , vol.31 , pp. 3832-3834
    • He, C.1    Zhang, M.Q.2    Wang, X.3
  • 6
    • 84903134982 scopus 로고    scopus 로고
    • Nucleosome eviction and multiple co-factor binding predict estrogen-receptor-alpha-associated long-range interactions
    • COI: 1:CAS:528:DC%2BC2cXhtVCjs7vL, PID: 24782518
    • He, C., Wang, X. and Zhang, M. Q. (2014) Nucleosome eviction and multiple co-factor binding predict estrogen-receptor-alpha-associated long-range interactions. Nucleic Acids Res., 42, 6935–6944
    • (2014) Nucleic Acids Res. , vol.42 , pp. 6935-6944
    • He, C.1    Wang, X.2    Zhang, M.Q.3
  • 7
    • 84951765264 scopus 로고    scopus 로고
    • 3CPET: finding co-factor complexes from ChIAPET data using a hierarchical Dirichlet process
    • PID: 26694485
    • Djekidel, M. N., Liang, Z., Wang, Q., Hu, Z., Li, G., Chen, Y. and Zhang, M. Q. (2015) 3CPET: finding co-factor complexes from ChIAPET data using a hierarchical Dirichlet process. Genome Biol., 16, 288
    • (2015) Genome Biol. , vol.16 , pp. 288
    • Djekidel, M.N.1    Liang, Z.2    Wang, Q.3    Hu, Z.4    Li, G.5    Chen, Y.6    Zhang, M.Q.7
  • 8
    • 84951567954 scopus 로고    scopus 로고
    • CTCFmediated human 3D genome architecture reveals chromatin topology for transcription
    • COI: 1:CAS:528:DC%2BC2MXitVSksb7F, PID: 26686651
    • Tang, Z., Luo, O. J., Li, X., Zheng, M., Zhu, J. J., Szalaj, P., Trzaskoma, P., Magalska, A., Wlodarczyk, J., Ruszczycki, B., et al. (2015) CTCFmediated human 3D genome architecture reveals chromatin topology for transcription. Cell, 163, 1611–1627
    • (2015) Cell , vol.163 , pp. 1611-1627
    • Tang, Z.1    Luo, O.J.2    Li, X.3    Zheng, M.4    Zhu, J.J.5    Szalaj, P.6    Trzaskoma, P.7    Magalska, A.8    Wlodarczyk, J.9    Ruszczycki, B.10
  • 10
    • 84922391809 scopus 로고    scopus 로고
    • A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions
    • Paulsen, J., Rø dland, E. A., Holden, L., Holden, M. and Hovig, E. (2014) A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions. Nucleic Acids Res., 42, e143
    • (2014) Nucleic Acids Res. , vol.42 , pp. 143
    • Paulsen, J.R.1    dland, E.A.2    Holden, L.3    Holden, M.4    Hovig, E.5
  • 11
    • 84940432398 scopus 로고    scopus 로고
    • Mango: a bias-correcting ChIA-PET analysis pipeline
    • COI: 1:CAS:528:DC%2BC28XhtlWmsbfN, PID: 26034063
    • Phanstiel, D. H., Boyle, A. P., Heidari, N. and Snyder, M. P. (2015) Mango: a bias-correcting ChIA-PET analysis pipeline. Bioinformatics, 31, 3092–3098
    • (2015) Bioinformatics , vol.31 , pp. 3092-3098
    • Phanstiel, D.H.1    Boyle, A.P.2    Heidari, N.3    Snyder, M.P.4
  • 13
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini YaH, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B Methodol. 57, 289–300
    • (1995) J. R. Stat. Soc. B Methodol. , vol.57 , pp. 289-300
    • Benjamini YaH, Y.1
  • 14
    • 84968468742 scopus 로고
    • Distribution functions and the Riemann Zeta function
    • Jessen, B. and Wintner, A. (1935) Distribution functions and the Riemann Zeta function. Trans. Am. Math. Soc., 38, 48–88
    • (1935) Trans. Am. Math. Soc. , vol.38 , pp. 48-88
    • Jessen, B.1    Wintner, A.2
  • 15
    • 84865800494 scopus 로고    scopus 로고
    • The long-range interaction landscape of gene promoters
    • COI: 1:CAS:528:DC%2BC38XhtlGnsLnM, PID: 22955621
    • 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
  • 16
    • 63849091245 scopus 로고    scopus 로고
    • Nextgeneration DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
    • COI: 1:CAS:528:DC%2BD1MXksVKns74%3D, PID: 19339662
    • Fullwood, M. J., Wei, C. L., Liu, E. T. and Ruan, Y. (2009) Nextgeneration 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
  • 17
    • 84861889354 scopus 로고    scopus 로고
    • Differential DNase I hypersensitivity reveals factordependent chromatin dynamics
    • COI: 1:CAS:528:DC%2BC38XoslSisLc%3D, PID: 22508765
    • He, H. H., Meyer, C. A., Chen, M. W., Jordan, V. C., Brown, M. and Liu, X. S. (2012) Differential DNase I hypersensitivity reveals factordependent chromatin dynamics. Genome Res., 22, 1015–1025
    • (2012) Genome Res. , vol.22 , pp. 1015-1025
    • He, H.H.1    Meyer, C.A.2    Chen, M.W.3    Jordan, V.C.4    Brown, M.5    Liu, X.S.6
  • 18
    • 84861095603 scopus 로고    scopus 로고
    • Topological domains in mammalian genomes identified by analysis of chromatin interactions
    • COI: 1:CAS:528:DC%2BC38XlslShurw%3D, PID: 22495300
    • 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
  • 19
    • 84868689387 scopus 로고    scopus 로고
    • Long distance relationships: enhancer–promoter communication and dynamic gene transcription
    • COI: 1:CAS:528:DC%2BC38XhslKqsrfP, PID: 23124110
    • Marsman J., Horsfield, J. (2012) Long distance relationships: enhancer–promoter communication and dynamic gene transcription. Biochim. Biophys. Acta, 1819:1217–1227
    • (2012) Biochim. Biophys. Acta , vol.1819 , pp. 1217-1227
    • Marsman, J.1    Horsfield, J.2
  • 22
    • 84866120986 scopus 로고    scopus 로고
    • Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages
    • COI: 1:CAS:528:DC%2BC38XhtlKltrnJ, PID: 22675074
    • Lan, X., Witt, H., Katsumura, K., Ye, Z., Wang, Q., Bresnick, E. H., Farnham, P. J. and Jin, V. X. (2012) Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages. Nucleic Acids Res., 40, 7690–7704
    • (2012) Nucleic Acids Res. , vol.40 , pp. 7690-7704
    • Lan, X.1    Witt, H.2    Katsumura, K.3    Ye, Z.4    Wang, Q.5    Bresnick, E.H.6    Farnham, P.J.7    Jin, V.X.8
  • 23
    • 84861964135 scopus 로고    scopus 로고
    • Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor
    • COI: 1:CAS:528:DC%2BC38XosVarsbg%3D, PID: 22682246
    • Deng, W., Lee, J., Wang, H., Miller, J., Reik, A., Gregory, P. D., Dean, A. and Blobel, G. A. (2012) Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell, 149, 1233–1244
    • (2012) Cell , vol.149 , pp. 1233-1244
    • Deng, W.1    Lee, J.2    Wang, H.3    Miller, J.4    Reik, A.5    Gregory, P.D.6    Dean, A.7    Blobel, G.A.8
  • 26
    • 84883583576 scopus 로고    scopus 로고
    • GWAS3D: Detecting human regulatory variants by integrative analysis of genomewide associations, chromosome interactions and histone modifications
    • PID: 23723249
    • Li, M. J., Wang, L.Y., Xia, Z., Sham, P.C., Wang, J. (2013) GWAS3D: Detecting human regulatory variants by integrative analysis of genomewide associations, chromosome interactions and histone modifications. Nucl. Acids Res. 41, W150–W158
    • (2013) Nucl. 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
  • 28
    • 84945574605 scopus 로고    scopus 로고
    • Epigenomic mapping and effect sizes of noncoding variants associated with psychotropic drug response
    • COI: 1:CAS:528:DC%2BC2MXhslSrurjE, PID: 26340055
    • Higgins, G. A., Allyn-Feuer, A. and Athey, B. D. (2015) Epigenomic mapping and effect sizes of noncoding variants associated with psychotropic drug response. Pharmacogenomics, 16, 1565–1583
    • (2015) Pharmacogenomics , vol.16 , pp. 1565-1583
    • Higgins, G.A.1    Allyn-Feuer, A.2    Athey, B.D.3
  • 32
    • 84937214946 scopus 로고    scopus 로고
    • Chromatin interaction analysis with paired-end tag (ChIA-PET) sequencing technology and application
    • Li, G., Cai, L., Chang, H., Hong, P., Zhou, Q., Kulakova, E. V., Kolchanov, N. A. and Ruan, Y. (2014) Chromatin interaction analysis with paired-end tag (ChIA-PET) sequencing technology and application. BMC Genomics, 15, S11
    • (2014) BMC Genomics , vol.15 , pp. S11
    • Li, G.1    Cai, L.2    Chang, H.3    Hong, P.4    Zhou, Q.5    Kulakova, E.V.6    Kolchanov, N.A.7    Ruan, Y.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.