Venn diagram illustrating the significantly affected genes (A, chartreuse color), isoforms (B, violet color) and differential promoter use (C, orange color) found in the LV <i>vs.</i> mock (I), Lena <i>vs.</i> mock (II) and LV <i>vs.</i> Lena (III) comparisons.

<p><b>I.</b> Venn diagram illustrating the significantly affected genes (A, 446), isoforms (B, 187) and differential promoter use (C, 14) found in the LV <i>vs.</i> mock comparison. <b>II.</b> Venn diagram illustrating the significantly affected genes (A, 153), isoforms (B, 72) and promoters (C, 6) found in Lena <i>vs.</i> mock comparison. <b>III.</b> Venn diagram illustrating the significantly affected genes (A, 241), isoforms (B, 34) and promoters (C, 7) found in LV <i>vs.</i> Lena comparison. The chartreuse circle, “A”, corresponds to the differentially expressed genes (I. LV <i>vs.</i> mock, II. Lena <i>vs.</i> mock and III. LV <i>vs.</i> Lena). The violet circle, “B”, represents the differentially expressed isoforms (I. LV <i>vs.</i> mock, II. Lena <i>vs.</i> mock and III. LV <i>vs.</i> Lena). The orange circle, “C”, corresponds to the differentially used promoters(I. LV <i>vs.</i> mock, II. Lena <i>vs.</i> mock and III. LV <i>vs.</i> Lena).</p

Venn diagram illustrating the significantly affected genes (I), isoforms (II), TSSs (III) and differential promoter use (VI) found in the LV <i>vs.</i> mock (A), Lena <i>vs.</i> mock (B) and LV <i>vs.</i> Lena (C) comparisons.

<p><b>I.</b> Venn diagram illustrating the significantly affected genes found in the LV <i>vs.</i> mock (A, 446), Lena <i>vs.</i> mock (B, 153) and LV <i>vs.</i> Lena (C, 241) comparisons. <b>II.</b> Venn diagram illustrating the significantly affected isoforms found in the LV <i>vs.</i> mock (A, 187), Lena <i>vs.</i> mock (B, 72) and LV <i>vs.</i> Lena (C, 34) comparisons. <b>III.</b> Venn diagram illustrating the significantly affected TSSs found in the LV <i>vs.</i> mock (A, 240), Lena <i>vs.</i> mock (B, 93) and LV <i>vs.</i> Lena (C, 50) comparisons. <b>VI.</b> Venn diagram illustrating the significantly affected promoters found in the LV <i>vs.</i> mock (A, 14), Lena <i>vs.</i> mock (B, 6) and LV <i>vs.</i> Lena (C, 7) comparisons. The blue circle, “A”, corresponds to the LV <i>vs.</i> mock case (I. significantly affected genes, II. significantly affected isoforms, III. significantly affected TSSs and VI. significantly affected promoters). The green circle, “B”, corresponds to the Lena <i>vs.</i> mock case (I. significantly affected genes, II. significantly affected isoforms, III. significantly affected TSSs and VI. significantly affected promoters). The purple circle, “C”, corresponds to the LV <i>vs.</i> Lena case (I. significantly affected genes, II. significantly affected isoforms, III. significantly affected TSSs and VI. significantly affected promoters).</p

Gene expression of <i>IFN-β</i> and <i>IFN-αω</i> genes in FPKM (Y axis).

<p>Top left: <i>IFN-β</i> expression in the mock, LV and Lena groups. <i>IFN-β</i> was differentially expressed between both the LV and Lena groups when compared to the mock infection group. <i>IFN-β</i> was also expressed at a significantly higher level in the LV group than in the Lena group. Lower right: <i>IFN-αω</i> expression in the mock, LV and Lena groups. <i>IFN-αω</i> was differentially expressed between the LV and Lena groups from one side and the mock group from the other side. <i>IFN-β</i> was also expressed at a significantly higher level in the LV group than in the Lena group.</p

Lists of the 5 top canonical pathways and the corresponding affected genes in the LV <i>vs.</i> mock (A), Lena <i>vs.</i> mock (B) and LV <i>vs.</i> Lena (C) comparisons.

<p><b>*</b>probability that a canonical pathway is significantly involved in the analysis.</p>£<p>number of genes in the list involved in a certain canonical pathway divided by the number of genes in the IPA database involved in the same canonical pathway.</p>&<p>genes involved in the corresponding canonical pathway.</p

Expression profiles of the genes involved in the 'metabolic pathways'.

<p>The X axis shows the time points following infection (days 5, 10 and 15 P.I). On the Y axis, genes expression fold changes.</p

Principal component analysis of RNA-seq data.

<p>Gene expression changes were investigated at days 5, 10 and 15 P.I. in honeybees infected (INF) with <i>N</i>. <i>ceranae</i> or no treatment (CR). The PCA was performed using normalized RNA-Seq data of 675 genes differentially expressed in at least one pairwise comparison: control vs infection at day 5 10 P.I or 15 P.I.Clear differences were seen between samples collected at days 5, 10 and 15 suggesting that ageing of the bees has a larger effect on the pattern of gene expression pattern than infection status.</p

Venn diagram illustrating the significantly affected genes (A), isoforms (B) and TSS (C) between infections at days 5, 10 and 15 P.I.

<p>Venn diagram illustrating the significantly affected genes (A), isoforms (B) and TSS (C) between infections at days 5, 10 and 15 P.I.</p