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tflink — TFLink transcription factor-target gene interactions (2022)

Description

Directed networks of the regulation of genes by transcription factors (TFs) in seven model organisms, from TFLink, which integrates the TF-target gene interactions of about 10 databases (e.g. ORegAnno, TRRUST, ReMap, GTRD, ChIP-Atlas, HTRIdb, PAZAR, TFe, Yeastract, modERN, REDfly, ...), from small-scale experiments (e.g. reporter assays, electrophoretic mobility shift assays, curated from the literature) and large-scale experiments (mostly ChIP-seq). An edge goes from a TF to a target gene whose expression it regulates, or to whose regulatory region it binds. The data are those of version 1.0 (April 2022) of TFLink.

There is one network per organism, with all its interactions (small and large scale): human (Homo sapiens), mouse (Mus musculus), rat (Rattus norvegicus), zebrafish (Danio rerio), fly (Drosophila melanogaster), worm (Caenorhabditis elegans) and yeast (Saccharomyces cerevisiae). The small-scale and large-scale subsets that TFLink also provides are those of the edges with small_scale true or false. The binding sites of the TFs are not included.

The networks have the following properties:

  • uniprot: the UniProt accession of the TF or target gene product.
  • gene_id: the NCBI Gene identifier of the gene (-1 if not given).
  • name: the name of the gene.
  • tflink_orthologs: the UniProt accessions of the orthologs of the node in the other organisms of TFLink, prefixed by the organism (e.g. Hs:Q15049), separated by ; (empty if none).
  • other_orthologs: the same, for the orthologs that are not in TFLink.
  • Edge detection_method: the methods of detection of the interaction, separated by ;.
  • Edge pubmed_ids: the PubMed identifiers of the publications of the interaction, separated by ;.
  • Edge source_databases: the databases from which the interaction comes, separated by ;.
  • Edge small_scale: whether the interaction is supported by small-scale experiments.
Tags
Biological Gene regulation Unweighted Metadata
Citation
  • O. Liska, B. Bohár, A. Hidas, T. Korcsmáros, B. Papp, D. Fazekas, E. Ari, "TFLink: an integrated gateway to access transcription factor-target gene interactions for multiple species." Database 2022, baac083 (2022) 10.1093/database/baac083 Sci-Hub
Upstream URL OK
https://tflink.net/
https://tflink.net/download/
Networks
Tip: click on a column header to sort the list, or hover over it for a description.
Column legend
$\left<k\right>$
Mean degree
$\sigma_k$
Standard deviation of the degrees
$\lambda_h$
Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$
Random walk mixing time
$r$
Degree assortativity
$c$
Global clustering coefficient
$\oslash$
(Pseudo-) diameter
$S$
Relative size of the largest component
NPs
Node properties
EPs
Edge properties
Name Nodes Edges $\left<k\right>$ $\sigma_k$ $\lambda_h$ $\tau$ $r$ $c$ $\oslash$ $S$ Kind Mode NPs EPs gt GraphML GML csv
human 20,147 6,739,357 334.51 1879.74 2368.92 0.77 -0.67 0.13 4 1.00 Directed Unipartite uniprot gene_id name tflink_orthologs other_orthologs detection_method pubmed_ids source_databases small_scale 6.9 MiB 33.5 MiB 33.2 MiB 25.2 MiB
mouse 21,597 4,057,582 187.88 1389.20 1791.15 1.82 -0.70 0.08 5 1.00 Directed Unipartite uniprot gene_id name tflink_orthologs other_orthologs detection_method pubmed_ids source_databases small_scale 2.8 MiB 17.7 MiB 17.6 MiB 13.4 MiB
rat 13,553 81,229 5.99 196.11 214.02 5.47 -0.75 0.00 6 1.00 Directed Unipartite uniprot gene_id name tflink_orthologs other_orthologs detection_method pubmed_ids source_databases small_scale 353 KiB 660 KiB 662 KiB 601 KiB
zebrafish 13,773 25,960 1.88 97.73 77.44 4.02 -0.57 0.00 5 1.00 Directed Unipartite uniprot gene_id name tflink_orthologs other_orthologs detection_method pubmed_ids source_databases small_scale 259 KiB 378 KiB 385 KiB 365 KiB
fly 18,775 368,629 19.63 349.24 454.99 2.08 -0.57 0.02 5 1.00 Directed Unipartite uniprot gene_id name tflink_orthologs other_orthologs detection_method pubmed_ids source_databases small_scale 619 KiB 1.9 MiB 1.9 MiB 1.5 MiB
worm 16,548 316,018 19.10 259.33 422.69 2.32 -0.61 0.03 5 1.00 Directed Unipartite uniprot gene_id name tflink_orthologs other_orthologs detection_method pubmed_ids source_databases small_scale 490 KiB 1.5 MiB 1.6 MiB 1.2 MiB
yeast 6,555 237,714 36.26 280.74 338.10 1.36 -0.43 0.04 4 1.00 Directed Unipartite uniprot gene_id name tflink_orthologs other_orthologs detection_method pubmed_ids source_databases small_scale 604 KiB 1.5 MiB 1.4 MiB 1.2 MiB