Extracting plants core genes responding to abiotic stresses by penalized matrix decomposition

Authors:
Jin-Xing Liu;Chun-Hou Zheng;Yong Xu
Affiliations:
Bio-Computing Research Center, Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen 518055, China and College of Information and Communication Technology, Qufu Normal University, Riz ...;College of Electrical Engineering and Automation, Anhui University, Hefei, Anhui 230039, China;Bio-Computing Research Center, Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen 518055, China
Venue:
Computers in Biology and Medicine
Year:
2012

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Abstract

Sparse methods have a significant advantage to reduce the complexity of genes expression data and to make them more comprehensible and interpretable. In this paper, based on penalized matrix decomposition (PMD), a novel approach is proposed to extract plants core genes, i.e., the characteristic gene set, responding to abiotic stresses. Core genes can capture the changes of the samples. In other words, the features of samples can be caught by the core genes. The experimental results show that the proposed PMD-based method is efficient to extract the core genes closely related to the abiotic stresses.