Cistrome Data Browser: A data portal for ChIP-Seq and chromatin accessibility data in human and mouse

Nucleic Acids Research

Volumn 45, Issue D1, 2017, Pages D658-D662

  Mei, Shenglin ^a   Qin, Qian ^a   Wu, Qiu ^a   Sun, Hanfei ^a   Zheng, Rongbin ^a   Zang, Chongzhi ^b,c   Zhu, Muyuan ^a   Wu, Jiaxin ^e   Shi, Xiaohui ^a   Taing, Len ^b   Liu, Tao ^f   Brown, Myles ^c,d   Meyer, Clifford A ^b,c   Liu, X Shirley ^a,b,c  

^a TONGJI UNIVERSITY   (China)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^c DANA FARBER CANCER INSTITUTE   (United States)

^d HARVARD MEDICAL SCHOOL   (United States)

^e TSINGHUA UNIVERSITY   (China)

^f UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ALGORITHM; ARTICLE; AUTOMATION; CHROMATIN IMMUNOPRECIPITATION; CISTROME DATA BROWSER; COMPUTER ANALYSIS; DATA BASE; EPIGENETICS; GENETIC TRANSCRIPTION; HUMAN; INFORMATION PROCESSING; NONHUMAN; REGULATORY MECHANISM; SEARCH ENGINE; ANIMAL; CHROMATIN ASSEMBLY AND DISASSEMBLY; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETIC EPIGENESIS; GENOMICS; HIGH THROUGHPUT SEQUENCING; MOUSE; PROCEDURES; WEB BROWSER;

ANIMALS; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN IMMUNOPRECIPITATION; DATABASES, GENETIC; EPIGENESIS, GENETIC; EPIGENOMICS; GENE EXPRESSION REGULATION; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICE; WEB BROWSER;

EID: 85015106384     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw983     Document Type: Article

References (28)

1. Park, P.J. (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat. Rev. Genet., 10, 669-680.
2. Furey, T.S. (2012) ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat. Rev. Genet., 13, 840-852.
3. Thurman, R.E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M.T., Haugen, E., Sheffield, N.C., Stergachis, A.B., Wang, H., Vernot, B. et al. (2012) The accessible chromatin landscape of the human genome. Nature, 489, 75-82.
4. Schmidt, D., Wilson, M.D., Spyrou, C., Brown, G.D., Hadfield, J. and Odom, D.T. (2009) ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods, 48, 240-248.
5. Song, L. and Crawford, G.E. (2010) DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harb. Protoc., 2010, doi:10.1101/pdb.prot5384.
6. Barski, A., Cuddapah, S., Cui, K., Roh, T.Y., Schones, D.E., Wang, Z., Wei, G., Chepelev, I. and Zhao, K. (2007) High-resolution profiling of histone methylations in the human genome. Cell, 129, 823-837.
7. Buenrostro, J.D., Giresi, P.G., Zaba, L.C., Chang, H.Y. and Greenleaf, W.J. (2013) Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods, 10, 1213-1218.
8. Barrett, T., Wilhite, S.E., Ledoux, P., Evangelista, C., Kim, I.F., Tomashevsky, M., Marshall, K.A., Phillippy, K.H., Sherman, P.M., Holko, M. et al. (2013) NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res., 41, D991-D995.
9. Edgar, R., Domrachev, M. and Lash, A.E. (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res., 30, 207-210.
10. Gibson, R., Alako, B., Amid, C., Cerdeno-Tarraga, A., Cleland, I., Goodgame, N., Ten Hoopen, P., Jayathilaka, S., Kay, S., Leinonen, R. et al. (2016) Biocuration of functional annotation at the European nucleotide archive. Nucleic Acids Res., 44, D58-D66.
11. Djebali, S., Davis, C.A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F. et al. (2012) Landscape of transcription in human cells. Nature, 489, 101-108.
12. Bernstein, B.E., Stamatoyannopoulos, J.A., Costello, J.F., Ren, B., Milosavljevic, A., Meissner, A., Kellis, M., Marra, M.A., Beaudet, A.L., Ecker, J.R. et al. (2010) The NIH Roadmap Epigenomics Mapping Consortium. Nat. Biotechnol., 28, 1045-1048.
13. 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.
14. Chacon, D., Beck, D., Perera, D., Wong, J.W. and Pimanda, J.E. (2014) BloodChIP: a database of comparative genome-wide transcription factor binding profiles in human blood cells. Nucleic Acids Res., 42, D172-D177.
15. Ziebarth, J.D., Bhattacharya, A. and Cui, Y. (2013) CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization. Nucleic Acids Res., 41, D188-D194.
16. Gerstein, M.B., Kundaje, A., Hariharan, M., Landt, S.G., Yan, K.K., Cheng, C., Mu, X.J., Khurana, E., Rozowsky, J., Alexander, R. et al. (2012) Architecture of the human regulatory network derived from ENCODE data. Nature, 489, 91-100.
17. Qin, Q., Mei, S., Wu, Q., Sun, H., Li, L., Taing, L., Chen, S., Li, F., Liu, T., Zang, C. et al. (2016) ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline.BMC Bioinformatics, 17, 404.
18. Meyer, C.A. and Liu, X.S. (2014) Identifying and mitigating bias in next-generation sequencing methods for chromatin biology. Nat. Rev. Genet., 15, 709-721.
19. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
20. Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., Nusbaum, C., Myers, R.M., Brown, M., Li, W. et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol., 9, R137.
21. Liu, T., Ortiz, J.A., Taing, L., Meyer, C.A., Lee, B., Zhang, Y., Shin, H., Wong, S.S., Ma, J., Lei, Y. et al. (2011) Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol., 12, R83.
22. Wang, S., Sun, H., Ma, J., Zang, C., Wang, C., Wang, J., Tang, Q., Meyer, C.A., Zhang, Y. and Liu, X.S. (2013) Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nat. Protoc., 8, 2502-2515.
23. Landt, S.G., Marinov, G.K., Kundaje, A., Kheradpour, P., Pauli, F., Batzoglou, S., Bernstein, B.E., Bickel, P., Brown, J.B., Cayting, P. et al. (2012) ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res., 22, 1813-1831.
24. Mendoza-Parra, M.A., Van Gool, W., Mohamed Saleem, M.A., Ceschin, D.G. and Gronemeyer, H. (2013) A quality control system for profiles obtained by ChIP sequencing. Nucleic Acids Res., 41, e196.
25. Speir, M.L., Zweig, A.S., Rosenbloom, K.R., Raney, B.J., Paten, B., Nejad, P., Lee, B.T., Learned, K., Karolchik, D., Hinrichs, A.S. et al. (2016) The UCSC Genome Browser database: 2016 update. Nucleic Acids Res., 44, D717-D725.
26. Zhou, X., Lowdon, R.F., Li, D., Lawson, H.A., Madden, P.A., Costello, J.F. and Wang, T. (2013) Exploring long-range genome interactions using the WashU Epigenome Browser. Nat. Methods, 10, 375-376.
27. Lee, T.I. and Young, R.A. (2013) Transcriptional regulation and its misregulation in disease. Cell, 152, 1237-1251.
28. Heintzman, N.D., Hon, G.C., Hawkins, R.D., Kheradpour, P., Stark, A., Harp, L.F., Ye, Z., Lee, L.K., Stuart, R.K., Ching, C.W. et al. (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature, 459, 108-112.