Ensembl regulation resources

Database

Volumn 2016, Issue , 2016, Pages

  Zerbino, Daniel R ^a   Johnson, Nathan ^a   Juetteman, Thomas ^a   Sheppard, Dan ^a,b   Wilder, Steven P ^a   Lavidas, Ilias ^a   Nuhn, Michael ^a   Perry, Emily ^a   Raffaillac Desfosses, Quentin ^a,c   Sobral, Daniel ^a,d   Keefe, Damian ^a   Gräf, Stefan ^a,e   Ahmed, Ikhlak ^a,f   Kinsella, Rhoda ^a   Pritchard, Bethan ^b   Brent, Simon ^b   Amode, Ridwan ^a,b   Parker, Anne ^a,b   Trevanion, Steven ^a,b   Birney, Ewan ^a   Dunham, Ian ^a   Flicek, Paul ^a,b   more..

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c PSL RESEARCH UNIVERSITY   (France)

^d INSTITUTO GULBENKIAN DE CIÊNCIA   (Portugal)

^e UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^f WEILL CORNELL MEDICAL COLLEGE   (Qatar)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; HISTONE;

ANIMAL; BIOLOGY; CHEMISTRY; DNA METHYLATION; DNA MICROARRAY; EPIGENETICS; GENETIC DATABASE; GENETIC EPIGENESIS; GENOME; GENOMICS; HUMAN; HUMAN GENOME; MOLECULAR GENETICS; MOUSE; PROCEDURES; PROTEIN MOTIF;

AMINO ACID MOTIFS; ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA; DNA METHYLATION; EPIGENESIS, GENETIC; EPIGENOMICS; GENOME; GENOME, HUMAN; GENOMICS; HISTONES; HUMANS; MICE; MOLECULAR SEQUENCE ANNOTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 84969940511     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bav119     Document Type: Article

References (60)

1. Jenuwein, T. and Allis, C.D. (2001) Translating the histone code. Science, 293, 1074-1080.
2. Klose, R.J. and Bird, A.P. (2006) Genomic DNA methylation: The mark and its mediators. Trends Biochem. Sci., 31, 89-97.
3. Weber, M., Hellmann, I., Stadler, M.B. et al. (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet., 39, 457-466.
4. Fraser, P. and Bickmore, W. (2007) Nuclear organization of the genome and the potential for gene regulation. Nature, 447, 413-417.
5. Grewal, S.I.S. and Jia, S. (2007) Heterochromatin revisited. Nat. Rev. Genet., 8, 35-46.
6. Jaenisch, R. and Bird, A. (2003) Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat. Genet., 33 (Suppl), 245-254.
7. Margueron, R., Trojer, P., and Reinberg, D. (2005) The key to development: Interpreting the histone code? Curr. Opin. Genet. Dev., 15, 163-176.
8. Maston, G.A., Evans, S.K., and Green, M.R. (2006) Transcriptional regulatory elements in the human genome. Annu. Rev. Genomics Hum. Genet., 7, 29-59.
9. Levine, M. and Tjian, R. (2003) Transcription regulation and animal diversity. Nature, 424, 147-151.
10. McLean, C.Y., Reno, P.L., Pollen, A.A. et al. (2011) Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature, 471, 216-219.
11. Freedman, M.L., Monteiro, A.N.A., Gayther, S.A. et al. (2011) Principles for the post-GWAS functional characterization of cancer risk loci. Nat. Genet., 43, 513-518.
12. Ren, B., Robert, F., Wyrick, J.J. et al. (2000) Genome-wide location and function of DNA binding proteins. Science, 290, 2306-2309.
13. Johnson, D.S., Mortazavi, A., Myers, R.M., and Wold, B. (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science, 316, 1497-1502.
14. Mikkelsen, T.S., Ku, M., Jaffe, D.B. et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature, 448, 553-560.
15. Keshet, I., Schlesinger, Y., Farkash, S. et al. (2006) Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat. Genet., 38, 149-153.
16. Lister, R., Pelizzola, M., Dowen, R.H. et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature, 462, 315-322.
17. Giresi, P.G., Kim, J., McDaniell, R.M. et al. (2007) FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res., 17, 877-885.
18. 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.
19. Buenrostro, J.D., Giresi, P.G., Zaba, L.C. et al. (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.
20. Barski, A., Cuddapah, S., Cui, K. et al. (2007) High-resolution profiling of histone methylations in the human genome. Cell, 129, 823-837.
21. Ernst, J., Kheradpour, P., Mikkelsen, T.S. et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature, 473, 43-49.
22. Hoffman, M.M., Ernst, J., Wilder, S.P. et al. (2013) Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res., 41, 827-841.
23. Esteller, M. and Herman, J.G. (2002) Cancer as an epigenetic disease: DNA methylation and chromatin alterations in human tumours. J. Pathol., 196, 1-7.
24. Adams, D., Altucci, L., Antonarakis, S.E. et al. (2012) BLUEPRINT to decode the epigenetic signature written in blood. Nat. Biotechnol., 30, 224-226.
25. Bernstein, B.E., Stamatoyannopoulos, J.A., Costello, J.F. et al. (2010) The NIH Roadmap Epigenomics Mapping Consortium. Nat. Biotechnol., 28, 1045-1048.
26. ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
27. Curwen, V., Eyras, E., Andrews, T.D. et al. (2004) The Ensembl automatic gene annotation system. Genome Res., 14, 942-950.
28. Chen, Y., Cunningham, F., Rios, D. et al. (2010) Ensembl Variation Resources. BMC Genomics, 11, 293.
29. Herrero, J., Muffato, M., Beal, K. et al. (2015) Ensembl comparative genomics resources. Database (Oxford), 2015, bav096.
30. Cunningham, F., Amode, M.R., Barrell, D. et al. (2015) Ensembl 2015. Nucleic Acids Res., 43, D662-D669.
31. Yates, A., Beal, K., Keenan, S. et al. (2015) The Ensembl REST API: Ensembl Data for Any Language. Bioinformatics, 31, 143-145.
32. Kinsella, R.J., Kahari, A., Haider, S. et al. (2011) Ensembl BioMarts: A hub for data retrieval across taxonomic space. Database (Oxford), 2011, bar030.
33. Zerbino, D.R., Wilder, S.P., Johnson, N. et al. (2015) The Ensembl Regulatory Build. Genome Biol., 16, 56.
34. Leinonen, R., Akhtar, R., Birney, E. et al. (2011) The European Nucleotide Archive. Nucleic Acids Res., 39, D28-D31.
35. Hoffman, M.M., Buske, O.J., Wang, J. et al. (2012) Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat. Methods, 9, 473-476.
36. Ernst, J. and Kellis, M. (2012) ChromHMM: Automating chromatin- state discovery and characterization. Nat. Methods, 9, 215-216.
37. Mathelier, A., Zhao, X., Zhang, A.W. et al. (2014) JASPAR 2014: An extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res., 42, D142-D147.
38. Altschul, S.F., Madden, T.L., Schaffer, A.A. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
39. Korhonen, J., Martinmä ki, P., Pizzi, C. et al. (2009) MOODS: fast search for position weight matrix matches in DNA sequences. Bioinformatics, 25, 3181-3182.
40. Stadler, M.B., Murr, R., Burger, L. et al. (2011) DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature, 480, 490-495.
41. Krueger, F. and Andrews, S.R. (2011) Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571-1572.
42. Vergoulis, T., Vlachos, I.S., Alexiou, P. et al. (2012) TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Res., 40, D222-D229.
43. 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.
44. Andersson, R., Gebhard, C., Miguel-Escalada, I. et al. (2014) An atlas of active enhancers across human cell types and tissues. Nature, 507, 455-461.
45. Forrest, A.R.R., Kawaji, H., Rehli, M. et al. (2014) A promoterlevel mammalian expression atlas. Nature, 507, 462-470.
46. Ballester, B., Johnson, N., Proctor, G., and Flicek, P. (2010) Consistent annotation of gene expression arrays. BMC Genomics, 11, 294.
47. Malone, J., Holloway, E., Adamusiak, T. et al. (2010) Modeling sample variables with an Experimental Factor Ontology. Bioinformatics, 26, 1112-1118.
48. Parker, A., Bragin, E., Brent, S. et al. (2010) Using caching and optimization techniques to improve performance of the Ensembl website. BMC Bioinformatics, 11, 239.
49. GrandienBackdahl,, Ljunggren, K., Gustafsson, M.O., and Berkenstam, J.A.A. (1995) Estrogen target tissue determines alternative promoter utilization of the human estrogen receptor gene in osteoblasts and tumor cell lines. Endocrinology, 136, 2223-2229.
50. McLaren, W., Pritchard, B., Rios, D. et al. (2010) Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics, 26, 2069-2070.
51. Robasky, K. and Bulyk, M.L. (2011) UniPROBE, update 2011: Expanded content and search tools in the online database ofprotein-binding microarray data on protein-DNA interactions. Nucleic Acids Res., 39, D124-D128.
52. Jolma, A., Yan, J., Whitington, T. et al. (2013) DNA-Binding Specificities of Human Transcription Factors. Cell, 152, 327-339.
53. Dostie, J. and Dekker, J. (2007) Mapping networks of physical interactions between genomic elements using 5C technology. Nat. Protoc., 2, 988-1002.
54. Fullwood, M.J., Liu, M.H., Pan, Y.F. et al. (2009) An oestrogenreceptor- Alpha-bound human chromatin interactome. Nature, 462, 58-64.
55. Lieberman-Aiden, E., van Berkum, N.L., Williams, L. et al. (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science, 326, 289-293.
56. Libbrecht, M.W., Ay, F., Hoffman, M.M. et al. (2015) Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression. Genome Res., 25, 544- 557.
57. Thurman, R.E., Rynes, E., Humbert, R. et al. (2012) The accessible chromatin landscape of the human genome. Nature, 489, 75-82.
58. Dixon, A.L., Liang, L., Moffatt, M.F. et al. (2007) A genome-wide association study of global gene expression. Nat. Genet., 39, 1202-1207.
59. Stranger, B.E., Forrest, M.S., Dunning, M. et al. (2007) Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science, 315, 848-853.
60. Schoenfelder, S., Furlan-Magaril, M., Mifsud, B. et al. (2015) The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements. Genome Res., 25, 1-16.