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,
of the original publications, name of the organism, source
databases, and indication about if the data were confirmed by
Interaction MITAB files contain transcription factor -
target gene interactions in HUPO-PSI MITAB 2.8 format.
The detailed description of the format and a header for MITAB
tables are available in the
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.
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.
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