5.5 Transcription Factor Databases 115
- Provide human protein interaction data precomputed from existing struc-
tural and experimental data using appropriate statistical methods.
- Provide integrated human protein interactions derived from the Biomolec-
ular Interaction Network Database (BIND) (Bader et al. 2003), DIP (Sal-
winski et al. 2004), and the Human Protein Reference Database (HPRD)
(Peri et al. 2004).
- Identify potential proteins from the databases that potentially interact
with proteins submitted by users. A score composed of three parts is
assigned to the predicted interaction data, and interactions with higher
scores indicate that the predictions are more reliable.
A set of online software tools has been developed to visualize and analyze
protein interaction networks.
5.5 Transcription Factor Databases
In humans, ribosomal RNA genes are transcribed by RNA polymerase I,
transfer RNA (tRNA) genes are transcribed by RNA polymerase III, and
protein-coding genes are transcribed by RNA polymerase II. Transcription
is initiated in the promoter region by a complex of different factors. The
following are the main transcription factor databases.
TRANSFAC transfac.gbf.de
The most complete transcription factor database is TRANSFAC (Wingender
et al. 1996). This database is concerned with eukaryotic transcription regula-
tion. It contains data on transcription factors, their target genes, and regula-
tory binding sites. The TRANSFAC database requires a license and fee, even
for noncommercial use. It uses a flat file format which can be browsed but
cannot be downloaded.
TRRD http://www.bionet.nsc.ru/trrd
The Transcription Regulatory Regions Database is a resource containing an
integrated description of gene transcription regulation. Each entry of the
database is concerned with one gene and contains data on localization and
functions of the transcription regulatory regions as well as gene expression
patterns (Kolchanov et al. 2002). TRRD contains only experimental data ob-
tained from annotations in scientific publications. TRRD release 6.0 contains
