is a Data Source.
REDfly (Regulatory Element Database for Drosophila and other insects) is a curated knowledgebase of insect transcriptional cis-regulatory sequences, including reporter-construct-defined cis-regulatory modules (CRMs), CRM segments, inferred and predicted CRMs, and transcription factor binding sites (TFBSs). Records are curated from the published literature with an emphasis on empirically validated elements, and include DNA sequence and coordinates, associated genes, and the expression patterns they direct annotated with anatomy ontology terms. Most data are for Drosophila melanogaster, with a growing number of other insect species. REDfly is developed by the Halfon lab and the Center for Computational Research at the University at Buffalo.
gene regulation, genomics, insects, model organisms, organisms
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| redfly.search | REDfly Search | options?sequence=1&assayed=1&cellCulture=1&range=10000 | Graphical Interface | http | REDfly search interface for querying ... |
| redfly.jbrowse | REDfly JBrowse | jbrowse | Graphical Interface | http | JBrowse genome browser displaying RED... |
| redfly.scrmshaw | REDfly SCRMshaw Predicted CRMs | options | Graphical Interface | http | Search interface for SCRMshaw-predict... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| tflink.downloads | TFLink Downloads | download | Product | http | had primary source | Download page listing interaction tab... |
| tflink.interactions.human | TFLink Human Interactions | TFLink_Homo_sapiens_interactions_All_simpleFormat_v1.0.tsv.gz (295.1 MB) | Graph | tsv | had primary source | All TF-target gene interactions for H... |
| tflink.interactions.mouse | TFLink Mouse Interactions | TFLink_Mus_musculus_interactions_All_simpleFormat_v1.0.tsv.gz (166.9 MB) | Graph | tsv | had primary source | All TF-target gene interactions for M... |
| tflink.interactions.rat | TFLink Rat Interactions | TFLink_Rattus_norvegicus_interactions_All_simpleFormat_v1.0.tsv (12.4 MB) | Graph | tsv | had primary source | All TF-target gene interactions for R... |
| tflink.interactions.zebrafish | TFLink Zebrafish Interactions | TFLink_Danio_rerio_interactions_All_simpleFormat_v1.0.tsv (3.3 MB) | Graph | tsv | had primary source | All TF-target gene interactions for D... |
| tflink.interactions.fly | TFLink Fruit Fly Interactions | TFLink_Drosophila_melanogaster_interactions_All_simpleFormat_v1.0.tsv (53.9 MB) | Graph | tsv | had primary source | All TF-target gene interactions for D... |
| tflink.interactions.worm | TFLink Nematode Interactions | TFLink_Caenorhabditis_elegans_interactions_All_simpleFormat_v1.0.tsv (46.2 MB) | Graph | tsv | had primary source | All TF-target gene interactions for C... |
| tflink.interactions.yeast | TFLink Yeast Interactions | TFLink_Saccharomyces_cerevisiae_interactions_All_simpleFormat_v1.0.tsv (42.1 MB) | Graph | tsv | had primary source | All TF-target gene interactions for S... |
| tflink.interactions.human.mitab | TFLink Human Interactions (MITAB) | TFLink_Homo_sapiens_interactions_All_mitab_v1.0.tsv.gz (218.9 MB) | Graph | psi_mi_mitab | had primary source | All human TF-target gene interactions... |
| tflink.gmt.human | TFLink Human TF Target Gene Sets | TFLink_Homo_sapiens_interactions_All_GMT_ncbiGeneID_v1.0.gmt (36.1 MB) | Product | tsv | had primary source | Human gene sets, one per transcriptio... |
| tflink.binding-sites.human | TFLink Human Binding Sites | TFLink_Homo_sapiens_bindingSites_All_annotation_v1.0.tsv.gz (153.1 MB) | Product | tsv | had primary source | Genomic locations of human TF binding... |
| tflink.binding-sites.human.gff3 | TFLink Human Binding Sites (GFF3) | TFLink_Homo_sapiens_bindingSites_All_annotation_v1.0.gff3 (913.7 MB) | Product | gff | had primary source | Human TF binding site locations as a ... |
| tflink.binding-sites.human.fasta | TFLink Human Binding Site Sequences | TFLink_Homo_sapiens_bindingSites_All_v1.0.fasta (1.1 GB) | Product | fasta | had primary source | Nucleotide sequences of human TF bind... |
REDfly (Regulatory Element Database for Drosophila and other insects) is a curated collection of insect transcriptional cis-regulatory sequences. It is a collaboration between Marc Halfon’s lab and the Center for Computational Research at the University at Buffalo, and is described most recently in Keränen et al. 2022 (Insects).
REDfly separates regulatory elements into reporter constructs (RCs, which define CRMs), CRM segments, inferred CRMs (derived from overlapping REDfly records), predicted CRMs (pCRMs, from computational or chromatin-based methods), and transcription factor binding sites (TFBSs). Records are curated from the literature and include sequence, coordinates, associated genes, supporting PubMed IDs, and the expression patterns that each element directs, annotated with Drosophila anatomy ontology terms for interoperability with FlyBase. Most records are for Drosophila melanogaster, with growing coverage of other insects. REDfly data are also shared with FlyBase and FlyMine.
The website (version 10) provides a search tool with downloads of selected records, a JBrowse genome browser, and a search interface for SCRMshaw-predicted CRMs across insect genomes. A legacy interface remains available for now. The application source code is on GitHub.
The REDfly database is licensed under CC BY-NC-ND 4.0, and its source code under GPL 3.0. Users are asked to cite the original publications for specific CRMs and TFBSs.
Created: October 10, 2026 | Last modified: October 19, 2026