Discretization of Expression Quantitative Trait Loci in Association Analysis Between Genotypes and Expression Data§

Andrés Masegosa, Rubén Armañanzas, María Abad-Grau, Víctor Potenciano, Serafín Moral, Pedro Larrañaga, Concha Bielza, Fuencisla Matesanz
2015 Current Bioinformatics  
Expression quantitative trait loci are used a s a tool t o identify genetic causes of natural variation In gene expression. Only In a few cases the expression o f a gene ls controlled b y a variant on a single genetic marker. There Is a plethora of different complexity levels of Interaction effects within markers, within genes and between marker and genes. This complexity challenges b!ostatlstlcians and b l o l nformatlt!ans every day and makes findings difficult to appear. As a way t o
more » ... analysis and better control confounders, we tried a new approach for association analysis between genotypes and expression data. We pursued t o understand whether discretization of expression data can be useful i n genome-transcrlptome association analyses. By discretlzlng the dependent variable, algorithms for learning classifiers from data as well as performing block selection were used to help understanding t h e relationship between the expression of a gene and genetic markers. We present the results of using this approach to detect new possible causes of expression variation of DRB5, a gene playing an Important role within the immune system. Together with expression of gene DRB5 obtained from the classical microarray technology, we have also measured DRB5 expression by using the more recent next-generation sequencing technology. A supplementary website including a link to the software with t h e method implemented can be found at http: //bios.ugr.es/DRB5.
doi:10.2174/157489361002150518123918 fatcat:mcieq7o5vbcvvonr2zkkl6cm54