Title: Prediction of regulatory gene pairs using dynamic time warping and gene ontology

Authors: Andy C. Yang; Hui-Huang Hsu; Ming-Da Lu; Vincent S. Tseng; Timothy K. Shih

Addresses: Department of Computer Science and Information Engineering, Tamkang University, New Taipei City, Taiwan ' Department of Computer Science and Information Engineering, Tamkang University, New Taipei City, Taiwan ' Department of Computer Science and Information Engineering, Tamkang University, New Taipei City, Taiwan ' Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan ' Department of Computer Science and Information Engineering, National Central University, Taoyuan, Taiwan

Abstract: Selecting informative genes is the most important task for data analysis on microarray gene expression data. In this work, we aim at identifying regulatory gene pairs from microarray gene expression data. However, microarray data often contain multiple missing expression values. Missing value imputation is thus needed before further processing for regulatory gene pairs becomes possible. We develop a novel approach to first impute missing values in microarray time series data by combining k-Nearest Neighbour (KNN), Dynamic Time Warping (DTW) and Gene Ontology (GO). After missing values are imputed, we then perform gene regulation prediction based on our proposed DTW-GO distance measurement of gene pairs. Experimental results show that our approach is more accurate when compared with existing missing value imputation methods on real microarray data sets. Furthermore, our approach can also discover more regulatory gene pairs that are known in the literature than other methods.

Keywords: microarray time series data; missing value imputation; gene regulation prediction; DTW; dynamic time warping; gene ontology; regulatory gene pairs; gene expressions; k-nearest neighbour; KNN; bioinformatics.

DOI: 10.1504/IJDMB.2014.064010

International Journal of Data Mining and Bioinformatics, 2014 Vol.10 No.2, pp.121 - 145

Received: 13 Feb 2012
Accepted: 13 Feb 2012
Published online: 21 Oct 2014 *

Full-text access for editors Full-text access for subscribers Purchase this article Comment on this article