Member-only story
Perform eQTL analysis using R package MatrixEQTL
What is eQTL analysis?
Full name of eQTL“ Expression Quantitative Trait Locianalysis”， I.e. ‘gene loci expressing quantity and position’, It refers to regions on chromosomes that can specifically regulate mRNA and protein expression levels, and the expression levels of mRNA/protein are proportional to quantitative traits. EQTL analysis is the study of the correlation between genetic mutations and gene expression by linking changes in gene expression levels and genotypes.
EQTL can be divided into two types: cis and trans. Generally speaking, cis eQTL refers to SNP loci that are very close to the regulated gene, Generally located in the upstream and downstream 1Mb region of the regulated gene, trans eQTL usually acts on genetic variation of local genes, while trans eQTL is a type of locus opposite to cis eQTL, usually far away from the regulated gene (See the figure below):
The essence of eQTL analysis is to use all DNA variation sites as independent variables, take turns using each mRNA expression level as the dependent variable, and use a large amount of individual data as samples for linear regression to obtain the relationship between each SNP site and each mRNA expression level.
