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REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila
Open accessAbstract
The REDfly database of Drosophila transcriptional cis-regulatory elements provides the broadest and most comprehensive available resource for experimentally validated cis-regulatory modules and transcription factor binding sites among the metazoa. The third major release of the database extends the utility of REDfly as a powerful tool for both computational and experimental studies of transcription regulation. REDfly v3.0 includes the introduction of new data classes to expand the types of regulatory elements annotated in the database along with a roughly 40% increase in the number of records. A completely redesigned interface improves access for casual and power users alike; among other features it now automatically provides graphical views of the genome, displays images of reporter gene expression and implements improved capabilities for database searching and results filtering. REDfly is freely accessible at http://redfly.ccr.buffalo.edu.
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Cited by
Whetzel, P. L., Noy, N. F., Shah, N. H., Alexander, P. R., Nyulas, C., Tudorache, T., & Musen, M. A. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr469 · Cited by 783
Enhancer loops appear stable during development and are associated with paused polymerase
Ghavi-Helm, Y., Klein, F. A., Pakozdi, T., Ciglar, L., Noordermeer, D., Huber, W., & Furlong, E. E. M. (2014) · Nature · doi:10.1038/nature13417 · Cited by 536
Bonn, S., Zinzen, R. P., Girardot, C., Gustafson, E. H., Perez-Gonzalez, A., Delhomme, N., Ghavi-Helm, Y., Wilczyński, B., Riddell, A., & Furlong, E. E. M. (2012) · Nature Genetics · doi:10.1038/ng.1064 · Cited by 502
TRRUST: a reference database of human transcriptional regulatory interactions
Han, H., Shim, H., Shin, D., Shim, J. E., Ko, Y., Shin, J., Kim, H., Cho, A., Kim, E., Lee, T., et al. (2015) · Scientific Reports · doi:10.1038/srep11432 · Cited by 462
The cis-regulatory dynamics of embryonic development at single-cell resolution
Cusanovich, D. A., Reddington, J. P., Garfield, D. A., Daza, R. M., Aghamirzaie, D., Marco-Ferreres, R., Pliner, H. A., Christiansen, L., Qiu, X., Steemers, F. J., et al. (2018) · Nature · doi:10.1038/nature25981 · Cited by 363
Metadata
- Authors
- Gallo, S. M., Gerrard, D. T., Miner, D., Simich, M., Des Soye, B., Bergman, C. M., & Halfon, M. S.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-10-21
- Volume
- 39
- Issue
- Database
- Pages
- D118-D123
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2021841129
- Cited by
- 179
- References
- 0
- FWCI
- 5.91
- Type
- journal article
- Language
- en
- Open access
- gold
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- Gallo, S. M., Gerrard, D. T., Miner, D., Simich, M., Des Soye, B., Bergman, C. M., & Halfon, M. S. (2011). REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Research. https://doi.org/10.1093/nar/gkq999
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