EnhancerAtlas: A resource for enhancer annotation and analysis in 105 human cell/tissue types

Bioinformatics

Volumn 32, Issue 23, 2016, Pages 3543-3551

  Gao, Tianshun ^a   He, Bing ^b   Liu, Sheng ^a   Zhu, Heng ^c,d   Tan, Kai ^b,e   Qian, Jiang ^a,c  

^a JOHNS HOPKINS UNIVERSITY   (United States)

^b CHILDREN S HOSPITAL OF PHILADELPHIA   (United States)

^c JOHNS HOPKINS UNIVERSITY   (United States)

^d JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENHANCER REGION; GENOMICS; HUMAN; MACHINE LEARNING; NUCLEIC ACID DATABASE; SOFTWARE;

DATABASES, NUCLEIC ACID; ENHANCER ELEMENTS, GENETIC; GENOMICS; HUMANS; MACHINE LEARNING; SOFTWARE;

EID: 85016229211     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw495     Document Type: Article

References (25)

1. Andersson,R. et al. (2014) An atlas of active enhancers across human cell types and tissues. Nature, 507, 455-461.
2. Arnold,C.D. et al. (2013) Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science, 339, 1074-1077.
3. Barrett,T. et al. (2013) Ncbi geo: archive for functional genomics data sets-update. Nucleic Acids Res., 41 (Database issue), D991-D995.
4. Consortium,E.P. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
5. Cotney,J. et al. (2012) Chromatin state signatures associated with tissuespecific gene expression and enhancer activity in the embryonic limb. Genome Res., 22, 1069-1080.
6. Fullwood,M.J. et al. (2009) An oestrogen-receptor-alpha-bound human chromatin interactome. Nature, 462, 58-64.
7. Gaulton,K.J. et al. (2010) A map of open chromatin in human pancreatic islets. Nat. Genet., 42, 255-259.
8. Ghavi-Helm,Y. et al. (2014) Enhancer loops appear stable during development and are associated with paused polymerase. Nature, 512, 96-100.
9. He,B. et al. (2014) Global view of enhancer-promoter interactome in human cells. Proc. Natl. Acad. Sci. USA, 111, E2191-E2199.
10. Heintzman,N.D. et al. (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature, 459, 108-112.
11. Heinz,S. et al. (2015) The selection and function of cell type-specific enhancers. Nat. Rev. Mol. Cell Biol., 16, 144-154.
12. Hnisz,D. et al. (2013) Super-enhancers in the control of cell identity and disease. Cell, 155, 934-947.
13. Jin,F. et al. (2013) A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature, 503, 290-294.
14. Kent,W.J. et al. (2002) The human genome browser at UCSC. Genome Res., 12, 996-1006.
15. Kim,T.K. et al. (2010) Widespread transcription at neuronal activity-regulated enhancers. Nature, 465, 182-187.
16. Ong,C.T. and Corces,V.G. (2011) Enhancer function: new insights into the regulation of tissue-specific gene expression. Nat. Rev. Genet., 12, 283-293.
17. Pennacchio,L.A. et al. (2013) Enhancers: five essential questions. Nat. Rev. Genet., 14, 288-295.
18. Qin,B. et al. (2012) Cistromemap: a knowledgebase and web server for chipseq and dnase-seq studies in mouse and human. Bioinformatics, 28, 1411-1412.
19. Quinlan,A.R. and Hall,I.M. (2010) Bedtools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841-842.
20. Roadmap Epigenomics,C. et al. (2015) Integrative analysis of 111 reference human epigenomes. Nature, 518, 317-330.
21. Spitz,F. and Furlong,E.E. (2012) Transcription factors: from enhancer binding to developmental control. Nat. Rev. Genet., 13, 613-626.
22. Thurman,R.E. et al. (2012) The accessible chromatin landscape of the human genome. Nature, 489, 75-82.
23. Visel,A. et al. (2007) Vista enhancer browser-a database of tissue-specific human enhancers. Nucleic Acids Res., 35 (Database issue), D88-D92.
24. Visel,A. et al. (2009) Chip-seq accurately predicts tissue-specific activity of enhancers. Nature, 457, 854-858.
25. Zhou,X. et al. (2011) The human epigenome browser at washington university. Nat. Methods, 8, 989-990.