Improving the accuracy of signal transduction pathway construction using level-2 neighbours
by Thomas K.F. Wong, T.W. Lam, S.M. Yiu, Simon C.K. Wong
International Journal of Bioinformatics Research and Applications (IJBRA), Vol. 6, No. 6, 2010

Abstract: In this paper, we consider the problem of reconstructing a pathway for a given set of proteins based on available genomics and proteomics information such as gene expression data. In all previous approaches, the scoring function for a candidate pathway usually only depends on adjacent proteins in the pathway. We propose to also consider proteins that are of distance two in the pathway (we call them Level-2 neighbours). We derive a scoring function based on both adjacent proteins and Level-2 neighbours in the pathway and show that our scoring function can increase the accuracy of the predicted pathways through a set of experiments. The problem of computing the pathway with optimal score, in general, is NP-hard. We thus extend a randomised algorithm to make it work on our scoring function to compute the optimal pathway with high probability.

Online publication date: Thu, 24-Feb-2011

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