SEA


NAR Molecular Biology Database Collection entry number 1838
Zhang, Yan; Wei, Yanjun; Zhang, Shumei; Shang, Shipeng; Zhang, Bin; Li, Song .; Wang, Xinyu; Wang, Fang `; Su, Jianzhong; Wu, Qion g; Liu, Hongbo
1. College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
2. School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China

Database Description

SEA (Super-Enhancer Archive, http://sea.edbc.org/) is a web based comprehensive resource focuses on the collection, storage and online analysis of super-enhancers. It focuses on integrating super-enhancers in multiple species and annotating their potential roles in the regulation of cell identity gene expression. The current release of SEA incorporates 83,996 super-enhancers computationally or experimentally identified in 134 cell types/tissues/diseases, including human (75,439, three of which were experimentally identified), mouse (5,879, five of which were experimentally identified), Drosophila melanogaster (1,774), and Caenorhabditis elegans (904). To facilitate data extraction, SEA supports multiple search options, including species, genome location, gene name, cell type/tissue, and super-enhancer name. The response provides detailed (epi)genetic information, incorporating cell type specificity, nearby genes, transcriptional factor binding sites, CRISPR-Cas9 target sites, evolutionary conservation, SNPs, H3K27ac, DNA methylation, gene expression, and TF ChIP-seq data. Moreover, analytical tools and a genome browser were developed for users to explore super-enhancers and their roles in defining cell identity and disease processes in depth.

Acknowledgements

This project was supported by grants from the National Natural Science Foundation of China, the Natural Science Foundation of Heilongjiang Province, the Innovation and Technology special Fund for researchers of Harbin Science and Technology Bureau, and the Innovation Research Fund for Graduate Students of Harbin Medical University.

References

1. Hnisz, D., Abraham, B.J., Lee, T.I., Lau, A., Saint-Andre, V., Sigova, A.A., Hoke, H.A. and Young, R.A. (2013) Super-enhancers in the control of cell identity and disease. Cell, 155, 934-947.
2. Whyte, W.A., Orlando, D.A., Hnisz, D., Abraham, B.J., Lin, C.Y., Kagey, M.H., Rahl, P.B., Lee, T.I. and Young, R.A. (2013) Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell, 153, 307-319.
3. Hnisz, D., Schuijers, J., Lin, C.Y., Weintraub, A.S., Abraham, B.J., Lee, T.I., Bradner, J.E. and Young, R.A. (2015) Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers. Molecular cell, 58, 362-370.
4. Loven, J., Hoke, H.A., Lin, C.Y., Lau, A., Orlando, D.A., Vakoc, C.R., Bradner, J.E., Lee, T.I. and Young, R.A. (2013) Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell, 153, 320-334. 5. Wei Y, Zhang S, Shang S, Zhang B, Li S, Wang X, Wang F, Su J, Wu Q, Liu H et al: SEA: a super-enhancer archive. Nucleic acids research 2015.


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