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|Title: ||SLIDER: A Generic Metaheuristic for the Discovery of Correlated Motifs in Protein-Protein Interaction Networks|
|Authors: ||BOYEN, Peter|
VAN DYCK, Dries
van Ham, Roeland C. H. J.
van Dijk, Aalt D. J.
|Issue Date: ||2011|
|Publisher: ||IEEE COMPUTER SOC|
|Citation: ||IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 8(5). p. 1344-1357|
|Abstract: ||Correlated motif mining (CMM) is the problem of finding overrepresented pairs of patterns, called motifs, in sequences of interacting proteins. Algorithmic solutions for CMM thereby provide a computational method for predicting binding sites for protein interaction. In this paper, we adopt a motif-driven approach where the support of candidate motif pairs is evaluated in the network. We experimentally establish the superiority of the Chi-square-based support measure over other support measures. Furthermore, we obtain that CMM is an NP-hard problem for a large class of support measures ( including Chi-square) and reformulate the search for correlated motifs as a combinatorial optimization problem. We then present the generic metaheuristic SLIDER which uses steepest ascent with a neighborhood function based on sliding motifs and employs the Chi-square-based support measure. We show that SLIDER outperforms existing motif-driven CMM methods and scales to large protein-protein interaction networks. The SLIDER-implementation and the data used in the experiments are available on http://bioinformatics.uhasselt.be.|
|Notes: ||[Boyen, P; Van Dyck, D; Neven, F] Hasselt Univ, B-3590 Diepenbeek, Belgium [Boyen, P; Van Dyck, D; Neven, F] Transnatl Univ Limburg, B-3590 Diepenbeek, Belgium [van Dijk, ADJ] Wageningen Univ & Res Ctr, Bioinformat Grp, NL-6708 PB Wageningen, Netherlands
firstname.lastname@example.org; email@example.com; firstname.lastname@example.org; email@example.com; firstname.lastname@example.org|
|ISI #: ||000292681800016|
|Type: ||Journal Contribution|
|Validation: ||ecoom, 2012|
|Appears in Collections: ||Research publications|
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