REDfly: The Regulatory Element Database for Drosophila and other insects
Authors: Soile V. E. Keränen 1; Andrew E. Bruno 2; Marc S. Halfon 3,4,5
Affiliations: 1) None; 2) Center for Computational Research, University at Buffalo-State University of New York, Buffalo, NY; 3) Departments of Biochemistry, Biomedical Informatics, and Biological Sciences, University at Buffalo-State University of New York, Buffalo, NY; 4) NY State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY; 5) Department of Molecular and Cellular Biology and Program in Cancer Genetics, Roswell Park Comprehensive Cancer Center, Buffalo, NY
Keywords: m. webtools and databases; e. enhancers
REDfly is a comprehensive knowledgebase of experimentally-validated cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs) for Drosophila and other insects, including the malaria mosquitoes Anopheles gambiae and Aedes aegypti and the beetle Tribolium castaneum. The database contains data on more than 53,500 regulatory sequences and almost 2700 TFBSs or their variants. Our goal is to include all functionally tested or predicted sequences, both with and without observable regulatory activity, to maximize the utility of the knowledgebase for purposes ranging from detailing the regulatory structure of a single locus, to large-scale studies of the regulatory genome, to providing training and/or validation data for machine-learning analyses of gene regulation. CRM data in REDfly are broadly segregated into three categories depending on the experimental evidence underlying their identification: reporter gene analysis, deletion of sequences from the genome, or predictions based on genomic assays such as ChIP-seq, ATAC-seq, and computational modeling. Finer-tuned filtering based on evidence type is possible through the ”advanced search” interface. An additional key REDfly feature is its extensive and searchable expression pattern annotation for each CRM’s activity using structured anatomy, staging, and biological process ontologies. Recently, REDfly has started to curate silencers, which inhibit gene transcription, in addition to the existing curation of both tested and predicted enhancers. Also new is a ”species” page that provides summaries of the data included for each species curated by REDfly, with BLAT and in silico PCR interfaces for each annotated genome. All REDfly code has been made open source. Future plans include updating REDfly’s search and download features to better serve our users, and providing a customized JBrowse interface for improved visualization and integration of REDfly data. REDfly is freely accessible at http://redfly.ccr.buffalo.edu and can be followed on Twitter at @REDfly_database.