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|Title: ||SLIDER: Mining correlated motifs in protein-protein interaction networks|
|Authors: ||BOYEN, Peter|
VAN DYCK, Dries
van Dijk, Aalt D.J.
van Ham, Roeland C.H.J.
|Issue Date: ||2009|
|Abstract: ||Correlated motif mining (CMM) is the problem to find overrepresented pairs of patterns, called motif pairs, in interacting protein sequences. 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 method SLIDER which uses local search with a neigborhood 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.|
|Type: ||Research Report|
|Appears in Collections: ||Research publications|
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