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	A network based covariance test for detecting multivariate eQTL in saccharomyces cerevisiae
	Yuan, Huili ; Li, Zhenye ; Tang, Nelson L. S. ; Deng, Minghua
	2016
关键词	eQTL Pathway Isoform CANONICAL CORRELATION-ANALYSIS PENALIZED LIKELIHOOD GENE EXPRESSION SELECTION DISEASE TRAITS CELL
英文摘要	Background: Expression quantitative trait locus (eQTL) analysis has been widely used to understand how genetic variations affect gene expressions in the biological systems. Traditional eQTL is investigated in a pair-wise manner in which one SNP affects the expression of one gene. In this way, some associated markers found in GWAS have been related to disease mechanism by eQTL study. However, in real life, biological process is usually performed by a group of genes. Although some methods have been proposed to identify a group of SNPs that affect the mean of gene expressions in the network, the change of co-expression pattern has not been considered. So we propose a process and algorithm to identify the marker which affects the co-expression pattern of a pathway. Considering two genes may have different correlations under different isoforms which is hard to detect by the linear test, we also consider the nonlinear test. Results: When we applied our method to yeast eQTL dataset profiled under both the glucose and ethanol conditions, we identified a total of 166 modules, with each module consisting of a group of genes and one eQTL where the eQTL regulate the co-expression patterns of the group of genes. We found that many of these modules have biological significance. Conclusions: We propose a network based covariance test to identify the SNP which affects the structure of a pathway. We also consider the nonlinear test as considering two genes may have different correlations under different isoforms which is hard to detect by linear test.; SCI(E); ARTICLE; 10
语种	英语
出处	SCI
出版者	14th Asia Pacific Bioinformatics Conference (APBC)
内容类型	其他
源URL	[http://hdl.handle.net/20.500.11897/459040]
专题	数学科学学院 生命科学学院
推荐引用方式 GB/T 7714	Yuan, Huili,Li, Zhenye,Tang, Nelson L. S.,et al. A network based covariance test for detecting multivariate eQTL in saccharomyces cerevisiae. 2016-01-01.

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