Promoters play an essential role in controlling gene expression. It is at this site
that the RNA polymerase binds for transcription. Understanding promoter strength
and regulation will enhance our understanding of gene expression. Multiple
functional sites are involved in the binding of the polymerase. Such elements as the
TATA box, GC box, CAAT box serve as binding sites for transcription factors.
By analyzing these individual elements within the promoter sites, as well as their
combinatorial effects, our understanding of promoter strength and regulation will be enhanced,
thus increasing our comprehension of gene expression.
Transcription factors play a central role in gene regulation and there are many
databases that are dedicated to them. These programs work with such databases to
predict and identify characteristics of the queried putative promoter sequences.
Mammalian Promoter Database (MPromDb) is an integrated novel database for gene promoters
with experimentally supported annotation of transcription start sites (TSS),
cis-regulatory elements,
CpG islands and ChIP-chip experimental results with intuitively visualized presentation.
The Eukaryotic Promoter Database at the Swiss Institute for Bioinformatics (SIB-EPD) is an
annotated non-redundant database of eukaryotic polymerase II promoters for which the
transcription start sites (TSS) have been determined.
The EPD also has a suite of signal search analysis programs.
TRANSFAC is the database on eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles.
JASPAR is a collection of transcription factor DNA-binding preferences, modelled as matrices.
ConSite allows the analysis of either one, or a number or, promoter sequences to find conserved transcription factor binding sites.
MatchTM is designed for searching potential binding sites for transcription factors (TF binding sites)
nucleotide sequences. MatchTM uses a library of mononucleotide weight matrices from TRANSFAC 6.0.
TESS is a web tool for predicting transcription factor binding sites in DNA sequences.
It can identify binding sites using site or consensus strings and positional weight matrices
from the TRANSFAC, JASPAR, IMD, and the CBIL-GibbsMat database.
The Over-represented Transcription Factor Binding Site (OTFBS) Prediction Tool tries to
detect over-represented motifs of known transcription factors in a set of upstream sequences
of similarly regulated genes. These genes can be clustered together with microarray data, or
just be genes from the same functional protein from a series of related species.
The CONFAC software finds the conserved Transcription Factor Binding Sites (TFBS) in the
promoter regions of the genes of given Human genes and the corresponding Mouse homolog.
The WeederH program in the suite of ModTools allows the discovery of transcription factor binding
sites and regulatory regions in sequences from homologous genes.
FIRE allows you to find novel regulatory elements that define (or are enriched in) a subset of genes.
Combines results from different motif finding programs to give you a statistically more significant result.
Genomatix is a commercial company that has a number of software tools and
databases related to promoter analysis. One of the more interesting things that
Genomatix can do is to find "frameworks" of transcription factor binding sites
that are commmon to a set of related sequences.
PolII promoters usually consist of multiple binding sites for transcription
factors which mediate the promoter function.
Frameworks are sets of
sequences that share a common orientation and distance organization between
a set of related sequences.
sample promoters file
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