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Advances in Bioinformatics
Volume 2014, Article ID 382452, 9 pages
http://dx.doi.org/10.1155/2014/382452
Research Article

Network Completion for Static Gene Expression Data

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan

Received 20 October 2013; Revised 3 February 2014; Accepted 24 February 2014; Published 26 March 2014

Academic Editor: Yves Van de Peer

Copyright © 2014 Natsu Nakajima and Tatsuya Akutsu. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

We tackle the problem of completing and inferring genetic networks under stationary conditions from static data, where network completion is to make the minimum amount of modifications to an initial network so that the completed network is most consistent with the expression data in which addition of edges and deletion of edges are basic modification operations. For this problem, we present a new method for network completion using dynamic programming and least-squares fitting. This method can find an optimal solution in polynomial time if the maximum indegree of the network is bounded by a constant. We evaluate the effectiveness of our method through computational experiments using synthetic data. Furthermore, we demonstrate that our proposed method can distinguish the differences between two types of genetic networks under stationary conditions from lung cancer and normal gene expression data.