This stusy was published in BIONFORMATICS 2005 May 1;21(9):1789-96.

Motivation:The 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 genome fractions.

Availability:F-values and real TFBS occurrences calculated for human, chimp, mouse, rat, zebrafish and fugu genomes are available for free download right here

Contact: abaranov@gmu.edu