is a Data Source.
HTRIdb (Human Transcriptional Regulation Interactions database) is an open-access database of experimentally verified interactions between human transcription factors and their target genes, developed at the Universidade Estadual Paulista (UNESP), Botucatu, Brazil. Each interaction records the TF and target gene symbols and NCBI Gene IDs, the experimental technique used to detect it, and the PubMed ID of the supporting article. At publication (2012) it held 51,871 interactions between 284 TFs and 18,302 target genes, curated from small- and mid-scale experiments in the literature and from ChIP-chip and ChIP-seq studies. The website has been did not respond when checked in October 2026; the most recent archived snapshot is from August 2022.
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| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| htridb.portal ⚠ | HTRIdb Web Interface | htri | Graphical Interface | http | HTRIdb web interface for searching hu... |
| htridb.downloads ⚠ | HTRIdb Downloads | pagdown.jsp | Product | http | HTRIdb download page offering all tra... |
| 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... |
HTRIdb (Human Transcriptional Regulation Interactions database) is a repository of experimentally verified interactions between human transcription factors (TFs) and their target genes. It was built by Luiz Bovolenta, Marcio Acencio, and Ney Lemke at the Instituto de Biociências de Botucatu, Universidade Estadual Paulista (UNESP), Brazil, and is described in Bovolenta et al. 2012 (BMC Genomics).
Note: As of 2026-10-19 the HTRIdb website does not respond. The most recent Internet Archive snapshot of the site is from August 2022.
Each interaction lists the TF and target gene symbols and NCBI Gene IDs, the detection technique, and the PubMed ID of the reporting article, along with protein-protein interactions of the TF and target. At publication, HTRIdb held 51,871 interactions between 284 TFs and 18,302 target genes. Of these, 2,283 came from small- and mid-scale techniques (such as EMSA, DNase I footprinting, and ChIP) curated from articles found through PubMed searches, and 49,588 came from ChIP-chip and ChIP-seq studies selected through the hmChIP database.
When online, the database could be searched through a web interface, with results downloadable as tab-delimited or spreadsheet files or viewed as networks in Cytoscape Web. Users could also submit new interactions. TFLink incorporated HTRIdb interactions into its integrated data set.
The publication describes HTRIdb as open access and freely available. No explicit data license was found.
Created: October 10, 2026 | Last modified: October 19, 2026