What is the TRANSFAC database? (Note: Lane no longer subscribes to Transfac Pro)

What is it?

As of August 2009, we longer license the professional version of TRANSFAC.
TRANSFAC Pro is a compilation of experimentally observed transcription factors (TF) and their properties.

As of October 2008, its data is now part of the BIOBASE Knowledge Library (BKL) database, with its analytical tools now available from the ExPlain component of BKL (see below for details). Note that BKL also includes the PROTEOME database.

What's in it?

Data on circa 10,000 transcription factors in species ranging from vertebrates to viruses.

• Transcription factor properties:
  • Structural features of a factor
  • Expression pattern
  • Regulatory network
  • Functional properties (what does it do)
  • Interacting factors
  • Position-specific matrices that can be used for similarity searching of DNA sequences that might bind a factor (e.g., using MEME and MAST).
• Genes that express transcription factors (example for androgen receptor).
• CHIP-on-chip data

Selected species covered by TRANSFAC:

• Homo sapiens
• Mus (several strains)
• Rattus novergicus
• Gallus gallus
• Saccharomyces cerevisiae
• Xenopus laevis
• Canis canis
• Oryctolagus cuniculus (rabbit)
• yeast (several strains)

What is it for?

Anthology databases such as TRANSFAC are excellent for quickly assessing the properties of biological objects (transcription factors in this case) because they compile the primary literature in a systematic manner. Typical TRANSFAC tasks include:

• Finding genes known to be regulated by a TF (example - old interface).
• Determining what regions of a gene are binding a TF.
• Obtaining the consensus DNA sequence(s) that bind a TF, as well as the position-specific matrix describing possible nucleotide substitutions.
• Performing sequence similarity searches using a processed version of the position-specific matrix provided by TRANSFAC.
• Identifying what collection of TFs interact with each other in regulating gene transcription.

Unique characteristics

TRANSFAC is the most comprehensive cross-species compilation of data regarding TFs.

Notes and caveats

• All records list the original literature from which the record was assembled.
• All data are derived from the primary experimental literature (no computational predictions). HOWEVER, TFs without a known binding site in species X are sometimes included on the basis of binding in species Y.
• Because of the size of the literature, always be cognizant that TRANSFAC (nor any other anthology database) should NOT be considered to be comprehensive or fully up to date.
• All records include a timestamp indicating when the record was last updated.
• Although it is an option, downloading of large segments of the database is not available under our current licensing terms. If you are interested in this capability, please a Lane Librarian.

Key references

• Class  Class slides from 2008 TRANSFAC workshop - old interface.
•  Videorecording from 2008 TRANSFAC workshop (note sound problems at the beginning of this recording) - old interface.
• BJK ExPlainmanual.
• Original paper: Matys, V. et al., (2006): TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes, Nucl Acids Res.
• All PubMed publications pertaining to TRANSFAC and published by the TRANSFAC group.
• Publications that feature BIOBASE products

Source

Lane Librarian

ypouliot, September 18, 2009