is a Data Source.
TRED (Transcriptional Regulatory Element Database) was a curated database of cis-regulatory elements, with an emphasis on transcription factor (TF) binding sites, TF-promoter regulatory interactions, and promoter annotations for human, mouse, and rat genes. It combined computational promoter prediction with literature-based manual curation of regulatory interactions, and was originally developed and hosted at Cold Spring Harbor Laboratory. TRED served as an upstream primary source for downstream regulatory network resources such as DoRothEA. The resource is now legacy and effectively superseded; its original hosting sites are no longer serving content, and it was dropped from some downstream tools due to licensing constraints.
Warning: No license entered
Unknown
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| tred.docs | TRED Publication | gkl1041 | Documentation | http | Reference publication describing TRED... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| dorothea.graph | DoRothEA Regulon Graph | v1.0.0 | Graph | r | had primary source | Core TF–target regulon knowledge grap... |
| 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... |
TRED was a curated database of transcriptional regulatory elements focused on transcription factor (TF) binding sites, TF-promoter regulatory interactions, and promoter annotations for human, mouse, and rat. It paired computational promoter prediction with literature-based manual curation, and was originally developed at Cold Spring Harbor Laboratory.
TRED is legacy and effectively superseded. Its historical hosting URLs (rulai.cshl.edu/TRED and a cb.utdallas.edu/TRED mirror) no longer serve the database, and the resource was removed from some downstream tools owing to licensing constraints. It is recorded here primarily for provenance, as an upstream primary source for resources such as DoRothEA.
Jiang C, Xuan Z, Zhao F, Zhang MQ. TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Res. 2007;35(Database issue):D137-D140. doi:10.1093/nar/gkl1041
Created: June 18, 2026 | Last modified: September 23, 2026