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For the mean gene count per NB-LRR tandem array, Aethionema scores highest.
The mean gene count score was 21.1 (SD 2.6) in people with type 2 diabetes and 20.5 (2.7) in those without type 2 diabetes (web table K).
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Figure 3A displays the result of the 26 genome analysis including a smoothed density plot of the shared gene count distributions, the mean value for each N, and the best-fit exponential decay.
A prediction model for bacterial richness based on the six bacterial species was applied in a receiver operating characteristic analysis as described previously, computing the sum of mean abundance of species with greater abundance in high gene count than in low gene count minus the sum of those with greater abundance in low gene count than in high gene count.
Let y ij be the observed read count for the i th gene in the j th sample where sample j belongs to treatment t(j) = 1, 2. Let σ i 2 and μ i be the variance and mean read count for gene i.
For each one of the 7128 genes, mean count number (transformed normalized) was calculated for each embryonic day.
Outliers as determined by gene count and alignment were excluded.
"Count" means the threshold of minimum gene counts belonging to an annotation term, and "EASE" is a modified Fisher Exact P value.
X-axis, log2-fold change (log2-fc) in gene expression after RA treatment; Y-axis, mean log2- count per million (log2-cpm) representing relative expression levels.
Raw gene counts were normalized by trimmed mean of M-values (TMM) normalization method in the edgeR package [ 45, 46].
Raw gene counts were normalized using weighted trimmed mean of M-values (i.e., calcNormFactors method "TMM") [ 39].
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