Introduction to TRANSFAC
TRANSFAC is a component of TRANSFAC Suite and presents information eukaryotic cis-acting regulatory DNA elements and trans-acting factors, in organisms ranging from yeast to humans.
The purpose of the TRANSFAC database is to:
- guide users through an overwhelming amount of data in a field
that is linked to nearly all areas of modern molecular
biology
- map the regulatory sites in individual genes and,
ultimately, in entire genomes
- furnish users with tools that can be used to identify
regulatory elements in newly-unravelled genomic sequences
- provide a basis for comprehensive understanding of how the genome governs transcriptional control
The majority of information in TRANSPATH has been manually curated from the primary literature. However, occasionally information has been curated from other compilations (Faisst and Meyer, Nucleic Acids Res. 20:3-26, 1992; Dhawale and Lande, Nucleic Acids Res 21:5537-5546, 1994), and each instance is clearly indicated.
A Brief History of TRANSFAC
TRANSFAC was created in 1988 as a printed compilation of protein
regulators of transcription (Wingender,
1988). Tables 1 and 2 of the printed compilation are the
foundation for TRANSFAC database, which was converted to an
electronic format in 1990 (BioTechForum - Advances in Molecular
Genetics, J Collins, AJ Driesel, eds. 4:95-108,
1991).
TRANSFAC Reports
TRANSFAC is made up of individual Reports for transcription factors and genes that either encode transcription factors or are regulated by them, transcription factor binding sites, fragments from ChIP on chip experiments, matrices, as described in the table below. Each Report, presented as a web page, is similarly structured and clearly labeled to orient the user.
The contents of each Report are described in detail in the documentation that follows. In general, TRANSFAC Reports comprise different blocks for curated Properties and References. The Properties blocks contains links to Property Reports that display additional details. Genes, proteins, and binding sites...etc. mentioned in a given Report are hyperlinked to the corresponding Reports. Click the Report names in the table below to access information about the structure of the various TRANSFAC Reports.
TRANSFAC Reports
| Report | Description |
|---|---|
| Locus | Contains details about a protein that regulates transcription through sequence-specific interactions with DNA and its corresponding gene that either encodes a transcription factor or is shown to be bound by a transcription factor |
| Functional Region | Contains details about regulatory regions of a gene, for which some functionality has been shown under certain conditions |
| Site | Contains information about sites within eukaryotic genes that are bound by transcription factors or complexes of transcription factors |
| Chip | Contains information about DNA fragments that have been shown to be bound by transcription factors in vivo using ChIP-chip or similar techniques |
| Matrix | Contains information about nucleotide distribution matrices for the binding sites of transcription factors |
Please note: TRANSFAC, TRANSPRO, TRANSCompel, and PathoDB are offered as a single product, TRANSFAC Suite, but are described separately because some of their features are unique to the particular database.
Other Important Features of TRANSFAC
Other important features of TRANSFAC are described below, and links to detailed information about these features are provided.
Classification of Transcription Factor Binding
TRANSFAC contains information about transcription factors that have been experimentally determined to bind DNA. Since some experimental methods are better than others, TRANSFAC provides a quality score that reflects the reliability of certain DNA-protein interactions. Details about the quality scale are provided here.
Additional Information about TRANSFAC
Additional information about TRANSFAC is provided below, with links to details.
Citing TRANSFAC
Instructions for citing TRANSFAC are provided here.
Printing TRANSFAC Reports
Instructions for printing TRANSFAC Reports are provided here.
TRANSFAC Publications
A list of publications about TRANSFAC is provided here.