Fig. 1
Differentially regulated genes in comparisons of ATG9‾, ATG16‾, and ATG9‾/16‾ strains with AX2. (A) Percentage of up- and downregulated genes in dependence of thresholds for fold change (2.0 ≥ FC ≤ 0.5) and pvalue ≤ 0.05 are shown. RNA was isolated from vegetative cells and nine biological replicates of each strain were analyzed. Transcriptome: 13,729 transcription units. (B) Venn diagrams of differentially regulated genes of ATG9‾ versus AX2 (left circle, blue), ATG16‾ versus AX2 (right circle, orange), and ATG9‾/16‾ versus AX2 (lower circle, grey). Differentially regulated genes common for two or three comparisons are shown in dark blue. Top, upregulated and bottom, downregulated genes. Only those genes with fold change ≥ 2.0 or ≤ 0.5 and p ≤ 0.05 were used as input. (C) Presentation of differentially regulated genes in a volcanoplot for each strain comparison. Differentially regulated genes with Log2 fold change ≥ 1 and p ≤ 0.05 are labelled red, genes with Log2 fold change ≤ − 1 and p ≤ 0.05 are labelled blue, differentially regulated autophagy related genes are highlighted by bigger orange-filled circles. For better visualization, all genes with a p-value between 10− 5 and 10− 6 are randomly distributed in the area from 10–5 to 10–6 and all genes with a p-value = 0 (i.e. values < 10− 6) are randomly distributed in the area from 10–6 and 10–7. Autophagy genes with a fold change ≥ 1.5 or ≤ 0.67 and p ≤ 0.05 in at least one of the comparisons are indicated by their Demerec name. The plot was created using the R environment (v. 2.15.0)