Database updated on 26-Jan-2017 with 423 changes

REDfly version 5.2.2 released!
REDfly now has the latest FlyBase anatomy ontology.
Regulatory Element Database for Drosophila v5.2.2

Release Notes
REDfly v5.2.2 Release Notes (March 17, 2017)
  • The FlyBase anatomy ontology has been updated to the 02/15/2017 release.
  • The BED batch download now contains sequence coordinates in the half-open system.
  • Predicted CRMs has been added to the search interface -- predicted CRM data will be coming soon.
  • A bug that removes special characters in PubMed citations has been fixed.
  • Many improvements has been made to the back-end of the application resulting in a more confident and robust deployment process.
REDfly v5.2.1 Release Notes (January 24, 2017)
  • 125 new CRMs from the cispatterns paper (PubMed ID 26377945) has been added to the database.
  • 152 new CRMs from the Fisher 2012 paper (PubMed ID 23236164) has been added to the database.
REDfly v5.2 Release Notes (January 6, 2017)
  • Calculation of inferred CRMs has been implemented (administrators only).
  • Inferred CRMs are now enabled. Inferred CRMs can only be browsed; searches is not implemented at this point.
  • Batch downloads now works again. Batch files can be downloaded in BED, CSV, FASTA, GFF3 and GBrowse formats for RCs, CRMs and TFBSes.
  • We have been querying the fly anatomy ontology via a database schema adapted to emulate an ontology. This has been replaced with an Apache Jena Fuseki SPARQL server, enabling us to query the ontology natively via SPARQL.
  • NCBI lookups was failing due to the switch from HTTP to HTTPS on their end. This has been fixed.
  • A thorough unit test suite has been developed for the new back end features.
  • The ontology data has been updated to include updates from the December 8, 2016 FlyBase fly anatomy ontology update.
  • The genes and features in the database has been updated based on the FB201605 release of the FlyBase genome data.
  • We have migrated to PHP 5.6 to take advantage of the new features and security updates -- PHP 5.5 has been end-of-lifed since July 2016.
  • We have completely migrated from PEAR to Composer for dependency management.
  • 57 new CRMs from the Jin 2013 paper (PubMed ID 23326246) has been added to the database.
  • There were also miscellaneous minor bug and security fixes, especially surrounding database access, concurrency and external service access.
REDfly v5.1.1 Release Notes (October 12, 2016)
  • Minor update to add a note to the search results informing the user that only 1,000 results are displayed.
REDfly v5.1 Release Notes (July 22, 2016)
  • All genome and other supporting data updated to FlyBase version FB2016_03
  • Add 10000+ cell-line only data
  • Add "exclude cell-line only" option when searching
  • Breakdown CRM numbers by category on homepage
  • Link to Fly Enhancers
  • Known Issues: Inferred CRM data is missing
REDfly v5.0 Release Notes (April 25, 2016)
  • Add "locus-based" search
  • Update lengths of chromosome X, 2R, 2L, 3R, 3L, 4. Add Y chromosome.
  • Update the Gene table as follows:
    • delete unused genes
    • update name and/or flybase id of remaining genes
    • update RC and BS names to reflect gene name change
    • repopulate the gene table with all the genes from FB2016_02
    • add another column to the gene table to indicate associated chromosome
  • Drop the features table and repopulate with only mRNA
  • Update the Expression Term table as follows:
    • delete unused expression terms
    • update name and/or id of remaining terms
    • add a column in the Expression Term table to indicate if a term is deprecated
    • repopulate the expression terms from the latest oncology data
  • Add missing FBtp terms to 855 RCs
  • Batch upload 129 RCs, 97 with images.
  • Make 13 citation entries ASCII compliant
  • Fix 75 RC names not having gene name in them
REDfly v4.1 Release Notes (October 05, 2015)
  • Records can now be downloaded in BED Simple and BED Browser format. The BED Browser format is annotated for use with the Genome Browser.
  • The SOAP-based web service used for fetching PubMed citation was TERMINATED on July 1, 2015. Code has been updated to use the current version of the Entrez Programming Utilities.
REDfly v4.0 Release Notes (February 18, 2015)
  • All entities have been updated to include R6 coordinates. While R3 and R4 coordinates are maintained for historical reasons, they will no longer be available for download. If you require R3 or R4 coordinates please contact us.
  • GBrowse link has been restored to the current FlyBase GBrowse2 implementation. At present, we are experiencing slow performance as the REDfly custom annotations load. Please bear with us as we work to find a speedier solution.
  • Genomic region snapshots in the "location" results tab have been restored. Only Genes, Transcripts, and CRMs are currently displayed.
  • Minor errors in the "Advanced Search" functions have been corrected.
REDfly v3.3 Release Notes (September 10, 2014)
  • Release v3.3 adds over 7830 new Reporter Constructs. This includes all of the Vienna Tile lines from Kvon et al. (2014) Nature 512(7512):91-5, PMID: 24896182. Note that because these lines have not been explicitly linked to target genes, the gene names in REDfly are given as "Unspecified." In future releases we will provide improved ways of searching for these lines as well as updated target gene information where possible.
  • The VT lines include "ubiquitous" as an expression term. As this term is not part of the Drosophila Anatomy Ontology, it will not appear in the "Expression" results tab. However, this information, along with staging information for expression patterns, is included in the "Notes" tab.
  • REDfly genome coordinates in this release remain at sequence version r5/dm3. We are in the process of updating to release 6 coordinates to bring REDfly back into harmony with the FlyBase genome annotation. At present, clicking the "GBrowse" link in the "Info" results pane links to the archived FlyBase FB2014_03 annotation. (If you are directed to the r6 GBrowse2 page, flush your browser cache or reload the page.) Also, until we have completed our migration to r6 coordinates, the "location" results tab has been disabled. We hope to have these updates completed in the near future. r5/dm3 coordinates will remain available for download for all entries.
  • We have fixed an error in how "minimization" status was being calculated.


Funded in part by the NSF and the NIGMS