DENdb: Database of integrated human enhancers

Database

Volumn 2015, Issue , 2015, Pages

  Ashoor, Haitham ^a   Kleftogiannis, Dimitrios ^a   Radovanovic, Aleksandar ^a   Bajic, Vladimir B ^a  

^a KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Saudi Arabia)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

DNA RESPONSIVE ELEMENT; GENETICS; HUMAN; METABOLISM; NUCLEIC ACID DATABASE; NUCLEOTIDE MOTIF;

DATABASES, NUCLEIC ACID; HUMANS; NUCLEOTIDE MOTIFS; RESPONSE ELEMENTS; TRANSCRIPTION FACTORS;

EID: 84943155486     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bav085     Document Type: Article

References (38)

1. Lee, T.I. and Young, R.A. (2000) Transcription of eukaryotic protein-coding genes. Annu. Rev. Genet., 34, 77-137.
2. Heintzman, N.D. and Ren, B. (2009) Finding distal regulatory elements in the human genome. Curr.Opin. Genet. Dev., 19, 541-549.
3. 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.
4. Plank, J.L. and Dean, A. (2014) Enhancer function: Mechanistic and genome-wide insights come together. Mol. Cell, 55, 5-14.
5. Shlyueva, D., Stampfel, G. and Stark, A. (2014) Transcriptional enhancers: From properties to genome-wide predictions. Nat. Rev. Genet., 15, 272-286.
6. ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
7. Bernstein, B.E., Stamatoyannopoulos, J.A., Costello, J.F. et al. (2010) The NIH Roadmap Epigenomics Mapping Consortium. Nat. Biotechnol., 28, 1045-1048.
8. 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.
9. FANTOM Consortium and the RIKEN PMI and CLST, Forrest, A.R., Kawaji, H. et al. (2014) A promoter-level mammalian expression atlas. Nature, 507, 462-470.
10. Johnson, D.S., Mortazavi, A., Myers, R.M. et al. (2007) Genomewide mapping of in vivo protein-DNA interactions. Science, 316, 1497-1502.
11. Kodzius, R., Kojima, M., Nishiyori, H. et al. (2006) CAGE: Cap analysis of gene expression. Nat. Methods, 3, 211-222.
12. Ernst, J. and Kellis, M. (2012) ChromHMM: Automating chromatin-state discovery and characterization. Nat. Methods, 9, 215-216.
13. 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.
14. Rajagopal, N., Xie, W., Li, Y. et al. (2013) RFECS: A random-forest based algorithm for enhancer identification from chromatin state. PLoS Comput. Biol., 9, e1002968.
15. Kleftogiannis, D., Kalnis, P. and Bajic, V.B. (2014) DEEP: A general computational framework for predicting enhancers. Nucleic Acids Res, 43, e6.
16. Firpi, H.A., Ucar, D. and Tan, K. (2010) Discover regulatory DNA elements using chromatin signatures and artificial neural network. Bioinformatics, 26, 1579-1586.
17. Erwin, G.D., Oksenberg, N., Truty, R.M. et al. (2014) Integrating diverse datasets improves developmental enhancer prediction. PLoS Comput. Biol., 10, e1003677.
18. Fletez-Brant, C., Lee, D., McCallion, A.S. et al. (2013) kmer-SVM: Aweb server for identifying predictive regulatory sequence features in genomic data sets. Nucleic Acids Res., 41, W544-W556.
19. Ghandi, M., Lee, D., Mohammad-Noori, M. et al. (2014) Enhanced regulatory sequence prediction using gapped k-mer features. PLoS Comput Biol., 10, e1003711.
20. Won, K.J., Zhang, X., Wang, T. et al. (2013) Comparative annotation of functional regions in the human genome using epigenomic data. Nucleic Acids Res., 41, 4423-4432.
21. 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.
22. Visel, A., Minovitsky, S., Dubchak, I. et al. (2007) VISTA Enhancer Browser-a database of tissue-specific human enhancers. Nucleic Acids Res., 35, D88-D92.
23. Qin, B., Zhou, M., Ge, Y. et al. (2012) CistromeMap: A knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. Bioinformatics, 28, 1411-1412.
24. Kulakovskiy, I.V., Medvedeva, Y.A., Schaefer, U. et al. (2013) HOCOMOCO: A comprehensive collection of human transcription factor binding sites models. Nucleic Acids Res., 41, D195-D202.
25. Wang, Z., Zang, C., Cui, K. et al. (2009) Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell, 138, 1019-1031.
26. Wang, Z., Zang, C., Rosenfeld, J.A., et al. (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet., 40, 897-903.
27. 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.
28. Thurman, R.E., Rynes, E., Humbert, R. et al. (2012) The accessible chromatin landscape of the human genome. Nature, 489, 75-82.
29. Grant, C.E., Bailey, T.L. and Noble, W.S. (2011) FIMO: Scanning for occurrences of a given motif. Bioinformatics, 27, 1017-1018.
30. Quinlan, A.R. and Hall, I.M. (2010) BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841-842.
31. Pruitt, K.D., Brown, G.R., Hiatt, S.M. et al. (2014) RefSeq: An update on mammalian reference sequences. Nucleic Acids Res., 42, D756-D763.
32. Teng, L., He, B., Wang, J. et al. (2015) 4DGenome: A comprehensive database of chromatin interactions. Bioinformatics., 31, 2560-2564.
33. Kheradpour, P., Ernst, J., Melnikov, A., et al. (2013) Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Genome Res., 23, 800-811.
34. Kumaki, Y., Ukai-Tadenuma, M., Uno, K.D., et al. (2008) Analysis and synthesis of high-amplitude Cis-elements in the mammalian circadian clock. Proc. Natl. Acad. Sci. U. S. A., 105, 14946-14951.
35. Ferretti, V., Poitras, C., Bergeron, D. et al. (2007) PReMod: A database of genome-wide mammalian cis-regulatory module predictions. Nucleic Acids Res., 35, D122-D126.
36. Navratilova, P., Fredman, D., Hawkins, T.A. et al. (2009) Systematic human/zebrafish comparative identification of cisregulatory activity around vertebrate developmental transcription factor genes. Dev. Biol., 327, 526-540.
37. Whyte, W.A., Orlando, D.A., Hnisz, D. et al. (2013) Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell, 153, 307-319.
38. Pott, S. and Lieb, J.D. (2015) What are super-enhancers? Nat. Genet., 47, 8-12.