Summary of the gene expression changes in the experiment.

<p>(A) Total number of differentially expressed (DE) genes in the contrasts. The numbers of up-regulated and down-regulated genes in each contrast are marked, respectively, as ↑ and ↓. An up-regulated gene level is higher at the head of the arrow showing the contrast; commonality is shown in brackets. The numbers of overrepresented GO Biological Process terms associated with the DE genes are shown in red italic characters for each contrast. (B) A geometrical visualization of the three-stage experimental process: shown are, with numbers of differentially expressed genes, the “orthogonal” stages, contrasts C to NV (black), NV to VL (red), VL to VH (blue), and the commonalities in the composite stages shown in the colour of the “orthogonal” contrast. The DE gene numbers in the composite contrasts without commonalities to the “orthogonal” stages are shown in grey. Commonalities between orthogonal stages are shown in corresponding colour in brackets. (C) Result of principal component analysis applied to a set 60 DE genes (pooled from all contrasts) with low adjusted <i>p</i>-values. Shown is a plot of the first two principal component scores for Cy3 and Cy5 replicates for all honeybee samples.