About

TFLink gateway uniquely provides comprehensive and highly accurate information on transcription factor - target gene interactions, nucleotide sequences and genomic locations of transcription factor binding sites for human and six model organisms: mouse (Mus musculus), rat (Rattus norvegicus), zebrafish (Danio rerio), fruit fly (Drosophila melanogaster), nematode (Caenorhabditis elegans), and yeast (Saccharomyces cerevisiae). TFLink contains clearly identified data, and provides information about the sources: databases, experimental methods and publications. To create TFLink, we examined the large transcription factor databases, and selected ten resources for integration: DoRothEA, GTRD, HTRIdb, JASPAR, ORegAnno, REDfly, ReMap, TRED, TRRUST, and Yeastract. By exploiting these database sources, we integrated accurate, small-scale experimental data and the results of large-scale experiments (see the FAQ for the detailed list of methods).

At the TFLink gateway you can Browse and search within the dataset, then open the Entry page of the selected transcription factor or target gene. Each entry page contains basic information about the protein or gene, its target genes and / or its transcription factors, binding site sequences, and crosslinks to proteins or genes at TFLink and to external databases and websites. You can download the interaction tables and binding site sequences of a certain protein or gene from the entry page, or download the content of the whole TFLink database at the Download page.

Publication

Liska O, Bohár B, Hidas A, Korcsmáros T, Papp B, Fazekas D, Ari E (2022) TFLink: An integrated gateway to access transcription factor - target gene interactions for multiple species. Database, baac083

Contact us

TFLink gateway was created by Orsolya Liska1,2, Balázs Bohár2,3, András Hidas2,4, Tamás Korcsmáros3,5,6, Balázs Papp1, Dávid Fazekas2,3 & Eszter Ari1,2

  1. Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, ELKH, Szeged, Hungary
    2.
  2. Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
    3.
  3. Earlham Institute, Norwich, UK
    4.
  4. Institute of Aquatic Ecology, Centre for Ecological Research, ELKH, Budapest, Hungary
    5.
  5. Quadram Institute Bioscience, Norwich, UK
    6.
  6. Imperial College London, Faculty of Medicine, London, UK
    7.

Please let us know if you have any questions or wish to integrate your data to TFLink:

tflink.net@gmail.com

Summary statistics of all small- and large-scale data

Organism Scale Nr. of TFs⁴ Nr. of target genes Nr. of interactions Nr. of binding sites⁵ Nr. of binding sequences
Homo sapiens small-scale 839 4,680 16,634 35,445 35,633
large-scale 1,348 20,120 6,722,723 8,857,060 8,870,892
total⁶ 1,606 20,139 6,739,357 8,892,505 8,906,525
Mus musculus small-scale 846 2,503 8,687 10,537 10,589
large-scale 711 21,263 4,048,895 363,228 380,417
total 1,156 21,536 4,057,582 373,765 391,006
Rattus norvegicus small-scale 6 6 8 179 196
large-scale 51 13,525 81,221 0 166
total 56 13,530 81,229 179 362
Danio rerio small-scale 0 0 0 0 0
large-scale 17 13,769 25,960 0 0
total 17 13,769 25,960 0 0
Drosophila melanogaster small-scale 173 281 699 3,262 6,026
large-scale 462 18,757 367,930 10,948 11,237
total 527 18,766 368,629 14,210 17,263
Caenorhabditis elegans small-scale 18 93 109 116 143
large-scale 282 16,499 315,909 9,746 9,905
total 289 16,519 316,018 9,862 10,048
Saccharomyces cerevisiae small-scale 191 2,166 5,349 5 5
large-scale 317 6,549 232,365 0 0
total 333 6,549 237,714 5 5
Total small-scale 2,073 9,729 31,486 49,544 52,592
large-scale 3,188 110,482 11,795,003 9,240,982 9,272,617
total 3,984 110,808 11,826,489 9,290,526 9,325,209
⁴ TF: transcription factor
⁵ In some cases the number of binding sites and the number of binding sequences are different because among the data we downloaded from JASPAR there are binding sequences with missing localization, for example when random sequences were investigated with the SELEX.
⁶ The total number of TFs, target genes, etc. can be different from the sum of small- and large-scale data due to overlapping items.