is a Data Source.
GTRD (Gene Transcription Regulation Database) is a database of uniformly annotated and processed next-generation sequencing data on gene transcription regulation, including ChIP-seq, ChIP-exo, DNase-seq, MNase-seq, ATAC-seq, FAIRE-seq, and RNA-seq from cells with altered transcription factor activity. Raw data are collected from GEO, SRA, ENCODE, and modENCODE, annotated with controlled vocabularies and ontologies, and processed with uniform workflows to produce transcription factor binding site peaks and meta-clusters, open chromatin regions and footprints, nucleosome positions, and predicted transcription factor target genes for nine species (human, mouse, rat, zebrafish, fruit fly, nematode, budding and fission yeast, and Arabidopsis). Data are available through a web interface, bulk downloads, and UCSC/Ensembl track hubs.
gene regulation, epigenomics, genomics, model organisms, organisms
Unknown
No external IDs available
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| gtrd.portal | GTRD Web Interface | gtrd.biouml.org | Graphical Interface | http | GTRD web interface for browsing and s... |
| gtrd.downloads | GTRD Downloads | current | Product | http | GTRD bulk download directory with pla... |
| gtrd.chip-seq_peaks | GTRD ChIP-seq Peaks | chip-seq | Product | http | Per-species archives of transcription... |
| gtrd.target_genes | GTRD Transcription Factor Target Genes | target_genes | Product | http | Per-species lists of transcription fa... |
| gtrd.track_hub | GTRD Track Hub | hub.txt (136 B) | Product | txt | UCSC-format track hub with GTRD bigBe... |
| 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... |
GTRD (Gene Transcription Regulation Database) collects public sequencing experiments related to transcription regulation and reprocesses them with uniform pipelines. It is developed by Fedor Kolpakov’s group at BIOSOFT.RU and the Federal Research Center for Information and Computational Technologies in Novosibirsk, Russia, on the BioUML platform and is described in Kolmykov et al. 2021 (Nucleic Acids Research).
Raw ChIP-seq, ChIP-exo, DNase-seq, MNase-seq, ATAC-seq, FAIRE-seq, and RNA-seq data are taken from GEO, SRA, ENCODE, and modENCODE and annotated with cell types, conditions, and target transcription factors using controlled vocabularies and ontologies. Uniform workflows produce TF binding peaks from several peak callers, merged meta-clusters, open chromatin regions and footprints, nucleosome positions, allele-specific binding events, and promoter-based TF target gene lists. Release 20.06 contained over 35,000 TF ChIP-seq experiments across nine species: human, mouse, rat, zebrafish, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Arabidopsis thaliana.
The web interface supports browsing and searching by TF, gene, cell type, or experiment. Bulk results are available from the downloads directory as plain-text intervals, metadata tables, bigBed files, and target gene lists, and GTRD tracks can be loaded into the UCSC or Ensembl genome browsers through a track hub.
The GTRD wiki states that the database may be used freely for non-commercial purposes as long as it is properly cited. Commercial users should contact gtrd@biosoft.ru to arrange a license.
Created: October 10, 2026 | Last modified: October 19, 2026