PUMA
Istituto di Informatica e Telematica     
Leoncini M., Montangero M., Pellegrini M., Tillan K. P. Composite Motif Finder: a combinatorial tool for finding cis-regulatory modules. Technical report, 2012.
 
 
Abstract
(English)
Controlling the differential expression of many thousands different genes at any given time is a fundamental task of metazoan organisms and this complex orchestration is controlled by the so-called regulatory genome encoding complex regulatory networks. Cis-Regulatory Modules (CRMs) are fundamental units of such networks. Intuitively CRMs are small stretches of DNA where several Transcription Factors bind so to perform in a cooperative manner a specific regulation task for nearby genes. The in silico prediction of CRMs is still an open problem, notwithstanding continuous progress and activity in the last two decades. In this paper we describe a new efficient combinatorial approach to the problem of detecting CRMs in promoter sequences, given in input a database of Transcription Factor Binding Sites encoded as PositionWeight Matrices. Testing with benchmark data from TRANSFAC we attain significant better average performance against nine state-of-the-art competing methods over 12 data sets, even at high level of "noise" in the data sets.
Subject Cis-Regulatory Module prediction
evaluation benchmark
combinatorial algorithm
F.2 ANALYSIS OF ALGORITHMS AND PROBLEM COMPLEXITY


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