Computational protocol: Familial resemblances in human whole blood transcriptome

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Protocol publication

[…] R software v2.14.1 (R Foundation for Statistical Computing; http://www.r-project.org) [] was used to compute the mean absolute correlation of raw gene expression levels between relative pairs across all 18,160 probes. For heritability analysis of gene expression and DNA methylation levels, corrections were made for the effects of microarray, position on microarray, sex, age, age2, sex*age, sex*age2, and blood cell counts (estimated cell counts for six cell types in methylation analyses and three cell types in gene expression analyses), using a standard least squares model in JMP software v12. We used residuals from this model to compute heritability estimates using the variance component method implemented in QTDT v2.6.1. [] We used full general models in which the variance in gene expression levels of each probe and DNA methylation levels of each CpG site were partitioned into polygenic effects (Vg), common environmental effects shared by family members (Vc), and non-shared environmental effects unique to each individual (Ve). We tested this full general model against a null model of no familial resemblance in which Vg = Vc = 0. We then computed mean maximal heritability, as the proportion of variance accounted by genetic and common environmental effects (Vg + Vc/Vg + Vc + Ve), mean genetic heritability, as the proportion of variance accounted by genetics effects (Vg/Vg + Vc + Ve), and the mean common environmental effect as the proportion of variance accounted by common environmental effects (Vc/Vg + Vc + Ve). Additionally, we computed heritability estimates in probes and CpG sites showing a significant familial effect (Vg and Vc significantly different from zero (P ≤ 0.05)). We computed FDR-corrected P-values to account for multiple testing. For comparison purposes, we computed alternative genetic models in which the variance in gene expression and DNA methylation levels was partitioned into Vg and Ve. We then computed mean genetic heritability, as the proportion of variance accounted by genetic effects (Vg/Vg + Ve).Phenotypic Pearson correlations between DNA methylation and gene expression levels were computed using R software v2.14.1 []. Assuming bivariate normal distribution, asymptomatic P-values were computed based on Fisher Z transformation as in Shakhbazov et al. for comparison purposes []. Genetic correlations between DNA methylation and gene expression were calculated using a bivariate analysis in SOLAR Eclipse version 7.6.4. Bonferonni corrections were used to account for multiple testing in phenotypic and genetic correlations. We used RCircos package and a modified version of the qqman package in R software to make the Circos plot and the chromosomic representations. []. Finally, we used the IPA system (Ingenuity® Systems, www.ingenuity.com) to analyze pathways overrepresented among genes of significant probes (n = 1211). […]

Pipeline specifications

Software tools QTDT, RCircos, qqman
Applications GWAS, Genome data visualization
Organisms Homo sapiens