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http://hdl.handle.net/1942/12110
Title: | SLIDER: A Generic Metaheuristic for the Discovery of Correlated Motifs in Protein-Protein Interaction Networks | Authors: | BOYEN, Peter VAN DYCK, Dries NEVEN, Frank van Ham, Roeland C. H. J. van Dijk, Aalt D. J. |
Issue Date: | 2011 | Publisher: | IEEE COMPUTER SOC | Source: | 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 peter.boyen@uhasselt.be; dries.vandyck@uhasselt.be; frank.neven@uhasselt.be; roeland.vanham@wur.nl; aaltjan.vandijk@wur.nl | Keywords: | Graphs and networks; biology and genetics | Document URI: | http://hdl.handle.net/1942/12110 | ISSN: | 1545-5963 | e-ISSN: | 1557-9964 | DOI: | 10.1109/TCBB.2011.17 | ISI #: | 000292681800016 | Category: | A1 | Type: | Journal Contribution | Validations: | ecoom 2012 |
Appears in Collections: | Research publications |
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preprint.pdf | Non Peer-reviewed author version | 1.2 MB | Adobe PDF | View/Open |
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