About REDfly

REDfly is a curated collection of known insect transcriptional cis-regulatory modules (CRMs), cis-regulatory module segments (CRMsegs), predicted cis-regulatory modules (pCRMs), and transcription factor binding sites (TFBSs). Our mission is to extract, accumulate, organize, annotate, and link the growing body of information on insect transcriptional cis-regulatory sequences, with an emphasis on empirically validated CRMs curated from the published literature. The majority of the data are for Drosophila melanogaster, but we also annotate an increasing number of other insects. Despite more than 20 years of experimental determination of these elements, the data have never been collected into a single searchable database. REDfly seeks to include all experimentally verified fly regulatory elements along with their DNA sequence, their associated genes, and the expression patterns they direct. Expression patterns are annotated using a defined anatomy ontology to enable high interoperability with FlyBase, FlyExpress, the BDGP in situ hybridization database, and other model organism resources.

If you know of experimentally verified cis-regulatory elements that are not included in the REDfly database, or have corrections to the archived data, please contact us.

REDfly has 0 CRMs (0 from in vivo reporter genes, 0 from cell-culture assays, and 0 from other evidence) associated with 0 genes, 0 CRMsegs associated with 0 genes, 0 pCRMs, and 0 TFBSs bound by 0 transcription factors acting on 0 target genes. These data are based on 0 curated publications.

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REDfly is a collaboration between the Halfon lab and the Center for Computational Research at the University at Buffalo.

The REDfly team respects the diversity of all individuals, regardless of race, ethnicity, sex, disability, religion, gender identification, or sexual orientation.

Using REDfly

Please see our User's Guide for more information.

Citing REDfly

When referencing specific CRMs, please be sure to include a reference to the original discoverers (cited in the "cite" tab or under "PMID" in the GFF-formatted download).

• Keränen, S.V.E., Villahoz-Baleta, A., Bruno, A.E., and Halfon, M.S. (2022). REDfly: An integrated knowledgebase for insect regulatory genomics. Insects, 13:618; doi: 10.3390/ insects13070618
• Rivera, John, Keränen, Soile V. E., Gallo, Steven M. and Halfon, Marc S. (2018). REDfly: the transcriptional regulatory element database for Drosophila. Nucleic Acids Res.; doi:10.1093/nar/gky957
• Gallo, S.M., Gerrard, D.T., Miner, D., Simich, M., Des Soye, B., Bergman, C.M. and Halfon, M.S. (2010). REDfly v3.0: Toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Res.; doi:39/suppl_1/D118/2509243
• Halfon, M.S., Gallo, S.M., and Bergman, C.M. (2008). REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila. Nucleic Acids Res. 36, D594-598; doi:36/suppl_1/D594/7632242
• Gallo, S. M., Li, L., Hu, Z. and Halfon, M. S. (2006). REDfly: a regulatory element database for Drosophila. Bioinformatics, Vol. 22 no. 3 2006, pages 381-383; doi:22/3/381/220380
• Bergman, C. M., Carlson, J. W. and Celniker, S. E. (2005). Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster. Bioinformatics, Vol. 21 no. 5 2005, pages 1747-1749; doi:21/8/1747/249595

REDfly licensing statement

The REDfly database is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives License v4 International (CC BY-NC-ND 4.0) and its underlying source code under a GNU General Public License v3 (GNU GPL 3.0). See disclaimer.

About our logo

The REDfly logo was designed by Alex Read as part of the GMOD Spring 2010 Logo Program.

Funding Support

REDfly is funded in part by National Institutes of Health grant R03 HD119839. Previous support was provided by NIH grant U24 GM142435 and R01 GM114067 and National Science Foundation grants DBI-1758252 and DBI-1355511.

Database

REDfly utilizes the MariaDB database. A schema diagram can be found here.

We would like to give special thanks to our student curators from the following classes:

• University at Buffalo BCH502 "Genome Annotation and Analysis" (2013)
• Baruch College (CUNY) BIO 4015 "Development Biology" (2019)
• Baruch College (CUNY) BIO 3005 "Molecular and Celullar Biology" and BIO 4015 "Development Biology" (2021)