important and challenging problems in molecular biology and bioinformatics. Here we present an algorithm that, given a set of promoters from co-regulated genes, identifies over-represented binding sites by using profiles (position specific frequency matrices) defining the sequence binding specificity of known TFs as well as matching statistics on a whole-genome level, bypassing the need of defining matching thresholds and/or the use of homologous sequences. Preliminary tests performed on experimentally validated sequence sets are very promising; moreover, the same algorithm is suitable also for the use with any model of the binding specificity of TFs.
Prediction of over represented transcription factor binding sites in co-regulated genes using whole genome matching statistics / G. Pavesi, F. Zambelli - In: Applications of fuzzy sets theory : 7th International Workshop on Fuzzy Logic and Applications, WILF 2007, Camogli, Italy, July 7-10, 2007 : proceedings / [a cura di] F. Masulli, S. Mitra, G. Pasi. - Berlin : Springer, 2007. - ISBN 9783540733997. - pp. 651-658 (( Intervento presentato al 7. convegno International Workshop on Fuzzy Logic and Applications (WILF) tenutosi a Camogli nel 2007.
|Titolo:||Prediction of over represented transcription factor binding sites in co-regulated genes using whole genome matching statistics|
PAVESI, GIULIO (Primo)
ZAMBELLI, FEDERICO (Ultimo)
|Settore Scientifico Disciplinare:||Settore INF/01 - Informatica|
|Data di pubblicazione:||2007|
|Digital Object Identifier (DOI):||http://dx.doi.org/10.1007/978-3-540-73400-0_83|
|Tipologia:||Book Part (author)|
|Appare nelle tipologie:||03 - Contributo in volume|