In order to test this hypothesis, we estimated the recombination rate in 1 Mb windows across the chicken genome and computed the average gene expression level and expression breadth for each non-overlapping window.
The density of Gypsy elements is significantly positively correlated with average gene expression levels, but is negatively correlated with both gene density and recombination.
The gene expression rate is based on the expression levels of the target gene versus the reference gene (ACT1).
The Agilent 44K provides the average gene expression levels in leaf blades during 17 developmental stages.
The gene expression ratio is given as the ratio of the target gene expression rate after heat treatment to that in non-treated controls.
Each bar represents average gene expression in three independent experiments.
The gene expression levels of PPET-1 and PPVIC were estimated as gene expression rates normalized by the expression of the house-keeping gene, glyceraldehyde-3-phosphate dehydrogenase.
Gene expression, rates of sequence divergence, and codon bias are correlated with the size of gene families, with large multicopy gene families having, on average, a lower expression level and breadth, lower codon bias, and higher rates of sequence divergence than single-copy gene families.
A similar approach has been utilized for processing gene expression profiles in [9]; it has been shown that averaged gene expression data within clusters have more predictive power than those from individual gene expressions.
Average gene set expression or single gene expression (counts or UMIs per 10,000 reads) was visualized using a customized FeaturePlot function with both color and size proportional to expression value plotted in ascending order of expression.
Although the majority of the 9406 genes analyzed showed relatively stable expression across different donors (for an average gene the expression level value of 95 out of a 100 individual fell within a 1.23-fold range), 2.6% of genes showed significant donor-to-donor variation, with a false discovery rate of 10%.
