About

TFLink database 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 freely available large transcription factor databases, and selected ten resources for integration: DoRothEA, GTRD, HTRIdb, JASPAR, ORegAnno, REDfly, ReMap, TRED, TRRUST, and Yeastract. From these source databases we integrated accurate, small-scale (such as DNase-I footprinting and EMSA) and large-scale approaches (e.g. ChIP-seq; see the FAQ for the detailed list of methods).

Contact us

Please write us if you have 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 35,483 35,717
large-scale 1,348 20,120 6,722,723 8,973,803 8,987,949
total⁶ 1,606 20,139 6,739,357 9,009,286 9,023,666
Mus musculus small-scale 846 2,503 8,687 10,559 10,611
large-scale 711 21,263 4,048,895 814,898 836,659
total 1,156 21,536 4,057,582 825,457 847,270
Rattus norvegicus small-scale 6 6 8 189 206
large-scale 51 13,525 81,221 0 244
total 56 13,530 81,229 189 450
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 3,223 6,016
large-scale 462 18,757 367,930 61,518 79,490
total 527 18,766 368,629 64,741 85,506
Caenorhabditis elegans small-scale 18 93 109 114 141
large-scale 282 16,499 315,909 23,695 32,886
total 289 16,519 316,018 23,809 33,027
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 49,573 52,696
large-scale 3,188 110,482 11,795,003 9,873,914 9,937,228
total 3,984 110,808 11,826,489 9,923,487 9,989,924

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.