Methylation-eQTL Analysis in Cancer Research.

Bioinformatics
Yusha LiuJeffrey S. Morris

Abstract

DNA methylation is a key epigenetic factor regulating gene expression. While promoter methylation has been well studied, recent publications have revealed that functionally important methylation also occurs in intergenic and distal regions, and varies across genes and tissue types. Given the growing importance of inter-platform integrative genomic analyses, there is an urgent need to develop methods to discover and characterize gene-level relationships between methylation and expression. We introduce a novel sequential penalized regression approach to identify methylation-expression quantitative trait loci (methyl-eQTLs), a term that we have coined to represent, for each gene and tissue type, a sparse set of CpG loci best explaining gene expression and accompanying weights indicating direction and strength of association. Using TCGA and MD Anderson colorectal cohorts to build and validate our models, we demonstrate our strategy better explains expression variability than current commonly used gene-level methylation summaries. The methyl-eQTLs identified by our approach can be used to construct gene-level methylation summaries that are maximally correlated with gene expression for use in integrative models, and produce a tissue-...Continue Reading

References

Feb 6, 2010·Genome Research·Louise LaurentChia-Lin Wei
Jan 27, 2011·PloS One·Fabienne BrenetJoseph M Scandura
May 30, 2012·Nature Reviews. Genetics·Peter A Jones
Aug 14, 2013·Biochimica Et Biophysica Acta·Marta KulisJosé I Martín-Subero
Sep 24, 2013·EURASIP Journal on Bioinformatics & Systems Biology·Elizabeth M JenningsVeerabhadran Baladandayuthapani
Jun 17, 2014·Bioinformatics·Wei ChengWei Wang
Feb 20, 2015·Nature·UNKNOWN Roadmap Epigenomics ConsortiumManolis Kellis
Oct 13, 2015·Nature Medicine·Justin GuinneySabine Tejpar
Nov 8, 2015·Bioinformatics·Marie Denis, Mahlet G Tadesse
Feb 9, 2017·Nucleic Acids Research·Christopher E SchlosbergJohn R Edwards
Nov 14, 2017·Nature Reviews. Genetics·Andrew E Teschendorff, Caroline L Relton

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