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

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Expression quantitative trait loci are used as a tool to identify genetic causes of natural variation in gene expression. Only in a few cases the expression of a gene is controlled by 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 biostatisticians and bioinformatitians every day and makes findings difficult to appear. As a way to simplify analysis and better control confounders, we tried a new approach for association analysis between genotypes and expression data. We pursued to understand whether discretization of expression data can be useful in genome-transcriptome association analyses. By discretizing the dependent variable, algorithms for learning classifiers from data as well as performing block selection were used to help understanding the 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 the method implemented can be found at http: //bios.ugr.es/DRB5.
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Keywords: RNA-seq; SNP; eQTL; gene expression microarray; machine learning

Document Type: Research Article

Publication date: April 1, 2015

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  • Current Bioinformatics aims to publish all the latest and outstanding developments in bioinformatics. Each issue contains a series of timely, in-depth reviews written by leaders in the field, covering a wide range of the integration of biology with computer and information science.

    The journal focuses on reviews on advances in computational molecular/structural biology, encompassing areas such as computing in biomedicine and genomics, computational proteomics and systems biology, and metabolic pathway engineering. Developments in these fields have direct implications on key issues related to health care, medicine, genetic disorders, development of agricultural products, renewable energy, environmental protection, etc.

    Current Bioinformatics is an essential journal for all academic and industrial researchers who want expert knowledge on all major advances in bioinformatics.
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