TRANSFAC® Release 7.0 - Documentation

TRANSFAC tables and their relations

The present release comprises the following ASCII flat files or tables:

SITE 7915 entries
GENE 2397 entries (1504 entries with SITE links)
FACTOR 6133 entries
CELL 1307 entries
CLASS 50 entries
MATRIX 398 entries

The contents of each table will be detailed below.

SITE gives information on (regulatory) transcription factor binding sites within eukaryotic genes. GENE gives a short explanation of the gene where a site (or group of sites) belongs to. FACTOR describes the proteins binding to these sites. CELL gives brief information about the cellular source of proteins that have been shown to interact with the sites. CLASS contains some background information about the transcription factor classes, while the MATRIX table gives nucleotide distribution matrices for the binding sites of transcription factors.

The ASCII flat file table SITE comprises all information which in the relational model is contained in distinct but connected records (SEQUENCES, METHOD, ENTRY and REFERENCE). Similarly, FACTOR, CLASS and MATRIX contain the full reference data. However, the factors binding to a certain site are indicated within the SITE entry by name and factor accession number, and vice versa the sites a certain factor binds to are likewise listed in the FACTOR records.



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