Gene interaction networks based on kernel correlation metrics. (1st January 2013)

• Record Type: Journal Article
• Authors: Cheng, Lijun; Khorasani, K.; Ding, Yongsheng; Guo, Xihong
• Is Part Of: International journal of computational biology and drug design. Volume 6:Number 1/2(2013)
• Page Start: 72
• Page End: 92
• Publication Date: 2013-01-01
• Subjects: gene interaction network -- KCC -- kernel correlation coefficient -- Pearson correlation -- yeast genes network -- Saccharomyces cerevisiae; Computational biology -- Periodicals; Drugs -- Design -- Periodicals; 570.285
• Languages: English
• ISSNs: 1756-0756

Abstract

In this paper, a Kernel correlation coefficient (KCC) method is proposed to elucidate the gene nonlinear relationships as a distance metric. To evaluate the performance of this nonlinear distance measure, a biological network of the Gaussian Kernel on a public dataset of yeast genes is constructed by using a graph theory. Specifically, the distribution and properties of this new measure are analysed and compared with the classical Pearson correlation method. The reliability and advantages of our proposed Kernel correlation metric is verified and shown formally on ten showcases of the DREAM (Dialogue for Reverse Engineering Assessments and Methods) project. Test experiment results demonstrate that the proposed Kernel correlation coefficient measure has a strong capability in identifying interaction genes, and that the proposed method can detect accurately the key genes and functional interactions (also known as the cliques) as compared to the commonly used Pearson correlation and Mutual Information measures.