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Gene expression quantitative trait methylation site

AD Anna Díez-Villanueva
MJ Mireia Jordà
RC Robert Carreras-Torres
HA Henar Alonso
DC David Cordero
EG Elisabet Guinó
XS Xavier Sanjuan
CS Cristina Santos
RS Ramón Salazar
RS Rebeca Sanz-Pamplona
VM Victor Moreno
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131 Normal samples (37 Healthy and 94 Adjacent) between gene expression and methylation were used to find the eQTMs performing the same analysis as for finding mQTLs (Additional File 1: Fig. 1). In the case of eQTMs, the association between methylation levels (M-value) and gene expression was tested adjusting by age, colon tissue site (right/left), tissue type (Healthy/Adjacent) and gender. A p-value threshold of 1.7e−08 (0.05/14,654 genes × 201 CpGs) was used. The number of CpGs was calculated as the median of CpGs at a maximum distance of 1 Mb for each gene (Fig. 1).

Independent eQTMs were calculated. For each gene, blocks of correlated (r2 > 0.3) cis-CpGs were created and eQTMs were defined by these CpG blocks. For each eQTM block based on independent CpGs, we choose the one with the minimum p-value as the representative eQTM of the block.

Copyright and License information: The Author(s) ©2021
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