is an Aggregator.
TFLink is an integrated gateway to transcription factor (TF) to target gene interactions, TF binding site locations, and binding site sequences for human and six model organisms (mouse, rat, zebrafish, fruit fly, nematode, and yeast). It integrates small-scale and large-scale experimental evidence from ten source databases, including TRRUST, GTRD, ReMap, JASPAR, and DoRothEA, recording the source database, detection method, and PubMed IDs for each record. Version 1.0 holds about 11.8 million interactions between 3,984 TFs and 110,808 target genes, available through a web interface and as downloadable tables and MITAB, GMT, GFF3, and FASTA files.
No external IDs available
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| tflink.browse | TFLink Browse | browse | Graphical Interface | http | Web interface for browsing and search... |
| tflink.downloads | TFLink Downloads | download | Product | http | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | Nucleotide sequences of human TF bind... |
| tflink.faq | TFLink FAQ | faq | Documentation | http | Frequently asked questions covering f... |
| tflink.website-code | TFLink Website Source | TFlink | Process | http | Source code of the TFLink website. |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| spoke.graph | SPOKE Graph | data-tools | Graph | http | had primary source | The SPOKE knowledge graph containing ... |
TFLink gathers transcription factor (TF) to target gene interactions and TF binding sites for human and six model organisms in one place. It was developed by researchers at the Biological Research Centre Szeged, Eötvös Loránd University, and the Earlham Institute, and is described in Liska et al. 2022 (Database).
Version 1.0 combines records from ten source databases: DoRothEA, GTRD, HTRIdb, JASPAR, ORegAnno, REDfly, ReMap, TRED, TRRUST, and Yeastract. Each interaction keeps its source database, detection method, and PubMed IDs, and is flagged as small-scale (low-throughput) or large-scale (high-throughput) evidence. Proteins and genes are identified by UniProt and NCBI Gene IDs. Human has the most data, about 6.7 million interactions among 1,606 TFs and 20,139 targets, followed by mouse (about 4.1 million). Zebrafish has only large-scale data.
Interactions can be browsed and searched on the website or downloaded per organism as simple tables, PSI-MI MITAB 2.8, and GMT gene sets. Binding sites are downloadable as tables, GFF3 annotations, and FASTA sequences. Each file type is split into small-scale, large-scale, and combined sets. The download files date from April 2022. The FAQ states that TFLink is freely available for non-commercial use.
Created: October 10, 2026 | Last modified: October 10, 2026