Title: A joint framework for missing values estimation and biclusters detection in gene expression data

Authors: Kin-On Cheng; Ngai-Fong Law; Yui-Lam Chan; Wan-Chi Siu

Addresses: Centre for Signal Processing, Department of Electronic and Information Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong ' Centre for Signal Processing, Department of Electronic and Information Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong ' Centre for Signal Processing, Department of Electronic and Information Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong ' Centre for Signal Processing, Department of Electronic and Information Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong

Abstract: DNA microarray experiment unavoidably generates gene expression data with missing values. This hardens subsequent analysis such as biclusters detection which aims to find a set of co-expressed genes under some experimental conditions. Missing values are thus required to be estimated before biclusters detection. Existing missing values estimation algorithms rely on finding coherence among expression values throughout the data. In view that both missing values estimation and biclusters detection aim at exploiting coherence inside the expression data, we propose to integrate these two steps into a joint framework. The benefits are twofold; the missing values estimation can improve biclusters analysis and the coherence in detected biclusters can be exploited for accurate missing values estimation. Experimental results show that the bicluster information can significantly improve the accuracy in missing values estimation. Also, the joint framework enables the detection of biologically meaningful biclusters.

Keywords: biclusters; bicluster detection; bioinformatics; gene expression data; missing values estimation; DNA microarrays.

DOI: 10.1504/IJBRA.2014.065243

International Journal of Bioinformatics Research and Applications, 2014 Vol.10 No.6, pp.574 - 586

Received: 30 Jun 2011
Accepted: 31 Aug 2012
Published online: 29 Apr 2015 *

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