A statistical analysis of the TRANSFAC database

Transcription factors are key regulatory elements that control gene expression. The TRANSFAC ® database represents the largest repository for experimentally derived transcription factor binding sites (TFBS). Understanding TFBS, which are typically conserved during evolution, helps us identify genomi...

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Bibliographic Details
Published in:BioSystems 2005-08, Vol.81 (2), p.137-154
Main Authors: Fogel, Gary B., Weekes, Dana G., Varga, Gabor, Dow, Ernst R., Craven, Andrew M., Harlow, Harry B., Su, Eric W., Onyia, Jude E., Su, Chen
Format: Article
Language:English
Subjects:
Algorithms
Amino Acid Motifs
Animals
Binding Sites
Cluster Analysis
Computational Biology - methods
Databases, Protein
Gene Expression Regulation
Gene regulation
Humans
Models, Statistical
Software
Statistics as Topic
Systems Biology
Transcription factor binding site
Transcription Factors - chemistry
Transcription, Genetic
TRANSFAC
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Summary:Transcription factors are key regulatory elements that control gene expression. The TRANSFAC ® database represents the largest repository for experimentally derived transcription factor binding sites (TFBS). Understanding TFBS, which are typically conserved during evolution, helps us identify genomic regions related to human health and disease, and regions that might be predictive of patient outcomes. Here we present a statistical analysis of all TFBS in the TRANSFAC ® database. Our analysis suggests that current definition of TFBS core regions in TRANSFAC ® should be re-examined so as to capture a more precise notion of “cores.” We offer insight into more appropriate definitions of TFBS consensus sequences and core regions. These revised definitions provide a better understanding of the nature of transcription factor-DNA binding and assist with developing algorithms for de novo TFBS discovery as well as finding novel variants of known TFBS.
ISSN:0303-2647
1872-8324
DOI:10.1016/j.biosystems.2005.03.003