REDfly: The regulatory sequence resource for Drosophila and other insects

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We have developed a unique resource, the REDfly (Regulatory Element Database for Fly) database of transcriptional regulatory elements, to provide regulatory annotation for the genome of Drosophila and other insects. The genomic sequences regulating gene expression—transcriptional cis-regulatory modules (CRMs, e.g. “enhancers”) and transcription factor binding sites (TFBSs)—are not currently curated by any other major database resources. This is a serious deficiency as CRMs play critical roles with respect to birth defects and chronic diseases as well as normal development, phenotypic variation, and evolution. Knowledge of experimentally validated CRMs and TFBSs is vital for many areas of research including interpretation and validation of data developed by large-scale genomics projects, providing training data for machine-learning CRM- discovery methods, genome annotation, modeling gene regulatory networks, studying the evolution of gene regulation, and numerous aspects of the basic biology of transcriptional regulation. Knowledge of insect CRMs is also an important step in developing biotechnology methods for control of insect disease vectors and for eliminating pathogen transmission. REDfly includes experimentally verified CRMs and TFBSs along with their DNA sequence, their associated genes, and the expression patterns they direct. It is the most detailed existing platform for metazoan regulatory element annotation and is widely acknowledged as the premier resource in the regulatory genomics arena. Only REDfly integrates all of the available insect cis-regulatory information from multiple sources to provide a comprehensive collection of regulatory elements. The objectives of this proposal are to keep REDfly up to date with the rapidly increasing numbers of CRMs and TFBSs being identified and to update the REDfly site to maximize its utility to the research community. The focus is on: (1) Curation. REDfly will continue to be kept up-to-date as new studies are published, and valuable data and metadata will be added to existing records. (2) User interface. We will develop more sophisticated search, display, and download capabilities to keep pace with the vastly increased amounts and types of data now contained in the database. We will update software components that have become obsolete in the decade since their initial implementation. (3) Data integration. We will increase integration of disparate data types and develop confidence scores for annotations. (4) Workflow. We will increase our curation efficiency and ability through improved workflows. (5) Ontology support. We will improve how we use biomedical ontologies through incorporating the latest ontology- related software, including ontology browsers and SPARQL queries. The proposed activities are significant as they will keep up-to-date a high-value resource for multiple research communities and increase REDfly’s utility by adding needed new features and functions. REDfly has already demonstrated its essential and unique value as an important platform for supporting hypothesis-driven empirical and computational research in multiple research areas. It will have greatly increased impact through the updates and enhancements proposed here.