This stusy was published in BIONFORMATICS 2005 May 1;21(9):1789-96.
detection of TFBS in genomic sequences is a basic
task for elucidating the transcriptional aspects
of gene regulation. Evaluation procedures applicable
to the TFBS prediction outputs needed improvement.
Predicted TFBS located outside of the transcription
associated areas often neglected from the functional
and the evolutionary points of view, therefore
deserving systematic overview.
Results:We calculated theoretical
occurrences of 184 TF binding sites according
to their PWMs and the dinucleotide statistics
of the completed vertebrate genomes, then performed
a TFBS prediction in the corresponding complete
genomic sequences and their repeat-free, repetitive
and regulatory fractions. Repeat-free fractions
of the closely related mammalian genomes were
characterized by strong similarities in TFBS occurrences.
A significant overrepresentation of multiple TFBS
was found in both repetitive and non-repetitive
Availability:F-values and real
TFBS occurrences calculated for human, chimp,
mouse, rat, zebrafish and fugu genomes are available
for free download right here