FAQ


Who worked on the TFLink project?
What does an entry page contain?
What does a transcription factor entry page contain?
What does a target gene entry page contain?
What does a transcription factor and target gene entry page contain?
What are the downloadable data formats?
What do interaction tables contain?
What do MITAB tables contain?
What is the MITAB format?
What do GMT files contain?
What do binding site tables contain?
What do binding site sequence files contain?
What source databases were used to create TFLink?
Is TFLink freely available?

Who worked on the TFLink project?

What does an entry page contain?

When you select a transcription factor or a target gene from the Browsing table an entry page will be opened. On each entry page the user can find basic information about the gene or protein: its gene name, Uniprot ID (linked to the corresponding Uniprot protein page), NCBI Gene ID (linked to the corresponding NCBI Gene database webpage), organism (the scientific name of the species), its function (transcription factor, target gene or both), the number of its interactions, and its orthologs (by the species name and its Uniprot ID) – if there is any. If the ortholog is also available at the TFLink database a link is provided to its TFLink entry page. Each entry page contains an interactive network visualization of interactions between the transcription factors and target genes. If there are more than 100 interactions available for a particular entry in TLink, we only show the first 100 targets / transcription factors / binding sites / binding site sequences on the website, but we make the full information available in the form of downloadable tables and fasta files.

What does a transcription factor entry page contain?

Besides basic information there is a table that contains information about the target genes of the transcription factor. If there are known binding sites of the transcription factor you will find a table containing their genomic locations and – for the small-scale experiments – a list containing their DNA sequences in fasta format below the table. The fasta files of the bindings sites are also downloadable for the small- and the large-scale experiments separately. (In some cases – among the data we downloaded from the JASPAR database – there are binding sequences with missing localization, for example when random sequences were investigated with the SELEX.) For an example please visit: https://tflink.net/protein/q9vhm6/

What does a target gene entry page contain?

Besides basic information there is a table that contains information about the transcription factors of the target gene. For an example please visit: https://tflink.net/protein/p52429/

What does a transcription factor and target gene entry page contain?

Some proteins act like transcription factors and target genes simultaneously. In some cases a transcription factor can regulate its own gene too. These entry pages contain similar information as simple transcription factor entry pages. For an example please visit: https://tflink.net/protein/p10242/

What are the downloadable data formats?

What do interaction tables contain?

Interaction table files are comma separated tables (csv) of transcription factor - target gene interactions that contain either interactions validated by small-scale experiments or large-scale experiments or these two data altogether. All tables contain the following data: Uniprot IDs, gene names, NCBI Gene IDs of transcription factors and target genes, names of the detection methods, Pubmed IDs of the original publications, name of the organism, source databases, and indication about if the data were confirmed by small-scale evidences. The interaction table files can be used as input data for the Cytoscape software to perform systems and network biology studies.

What do MITAB tables contain?

Interaction MITABs contain transcription factor - target gene interactions in HUPO-PSI MITAB 2.8 format.

What is the MITAB format?

MITAB 2.8 is a standardized format introduced by the Human Proteome Organization (HUPO) which captures binary molecular interactions using standardized content and vocabulary. The MITAB files are tab-delimited tables containing 46 columns. A header for the MITAB tables is available here.
For more information on the HUPO-PSI's molecular interaction format see: link
Sivade Dumousseau M et al. (2019) Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions. BMC Bioinformatics 19(1):134. doi: 10.1186/s12859-018-2118-1. The MITAB table files can be used as input data for the Cytoscape software to perform systems and network biology studies.

What do GMT files contain?

Interaction GMT (Gene Matrix Transposed) is a tab delimited file format that describes gene sets – target genes of a transcription factor – in each row. The first and second column contains information about the transcription factors (various IDs and gene names). The first cell in each row is always unique. From the third to the last column the target genes of the transcription factor are listed. The number of target genes can vary from transcription factor to transcription factor, therefore the number of cells can be different in every row. The user can choose between GMT files with Uniprot IDs, NCBI Gene IDs, and gene names. The GMT files are useful for enrichment and gene overrepresentation analyses and can be an input file for the MulEA and GSEA software.

What do binding site tables contain?

Binding site table files are comma separated tables (csv) of binding site annotations that contain unique TFLink IDs of binding sites, Uniprot IDs and gene names of the transcription factors, the names of the detection method, indication if it is a small- or a large-scale method, Pubmed IDs of the original publications, the organism, the source database, the version of the genome assembly, the name of the chromosome, the start and end coordinates of the sites, and the coding strand.

What do binding site sequence files contain?

Binding site sequence files are fasta files containing the DNA sequences of the transcription factor binding sites. The header of each sequence contains the unique internal TFLink ID of the binding site, the Uniprot ID and gene name of the transcription factor, the version of the genome assembly, the name of the chromosome, and the start and end coordinates of the sites.

What source databases were used to create TFLink?

We use the following abbreviations in the table:
Data based on small-scale experiments: SS
Data based on large-scale experiments: LS
Homo sapiens: Hs
Mus musculus: Mm
Rattus norvegicus: Rn
Danio rerio: Dr
Drosophila melanogaster: Dm
Caenorhabditis elegans: Ce
Saccharomyces cerevisiae: Sc
Nr. of data downloaded
Version Downloading date Type of data Nr. of integrated data Species
DoRothEA 2 19/06/2020 SS interactions 3,453 Hs
GTRD 20.06 202/07/2020 LS interactions 10,685,122 Hs, Mm, Rn, Dr, Ce, Sc
HTRIdb 1 29/04/2017 SS interactions 2,020 Hs
LS interactions 47,140
JASPAR 2020 22/07/2020 SS binding sites 3,123 Hs, Mm, Rn, Dm, Ce
LS binding sites 9,264,571
ORegAnno 2016 (the website is out of order) 24/05/2017 SS interactions 1,979 Hs, Mm, Rn, Dm, Ce, Sc
LS interactions 160,096
SS binding sites 47,344
LS binding sites 672,630
REDfly 6.0.2 16/06/2020 SS interactions 683 Dm
LS interactions 90
SS binding sites 2,229
LS binding sites 27
ReMap 2018 (v1.2) 16/07/2018 LS interactions 2,933,177 Hs
TRED obtained from RegNetwork 2017 06/08/2018 SS interactions 8,693 Hs, Mm
TRRUST 2 30/07/2018 SS interactions 16,570 Hs, Mm
Yeastract - 29/06/2017 SS interactions 5,349 Sc
LS interactions 188,072

Is TFLink freely available?

TFLink is freely available for non-commercial use.