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Bioinformatics Advance Access published online on February 4, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti307
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received August 11, 2004
Revised January 7, 2005
Accepted February 2, 2005

Article

A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areas

Maria Stepanova 1, Tatiana Tiazhelova 2, Mikle Skoblov 1, and Ancha Baranova 3*

1 Vavilov Institute of General Genetics, Gubkina str, 3, GSP-1, 111991, Moscow, Russia
2 Vavilov Institute of General Genetics, Gubkina str, 3, GSP-1, 111991, Moscow, Russia; Russian Center of Haematology, Moscow 125167, Russia
3 Center for Biomedical Genomics and BioInformatics, Molecular and Microbiology Department, College of Arts and Sciences, George Mason University, Fairfax, VA, 22031, USA; Vavilov Institute of General Genetics, Gubkina str, 3, GSP-1, 111991, Moscow, Russia

* To whom correspondence should be addressed.
Ancha Baranova, E-mail: abaranov{at}gmu.edu


  Abstract

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 need 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 at http://www.gmu.edu/departments/mmb/baranova/pages/bioinformatics.


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