Fig. 4
From: Enhanced protein secretion in reduced genome strains of Streptomyces lividans
Differential expression of genes between S. lividans TK24 and RG1.9 strains. (A) MA-plot for RNA-Seq datasets comparing S. lividans TK24 and RG1.9 strains. Genes similarly regulated in both strains (grey) and up- (red) or down- (blue) regulated in RG1.9 are indicated (M > 1 or M <-1 respectively; adjusted p-value < 0.05). M and A values were calculated as indicated (Material and Methods). For the 10 most prominently up- / down- regulated genes their SLIV/SCO gene IDs are indicated. (B) Differential expression of genes encoding proteins with the indicated biological function (as described, [52]) in S. lividans TK24 (grey) and RG1.9 (black) strains. For each strain and each functional group, the ratio ‘number of differentially expressed genes / total number of genes’ was plotted. (C) Heatmap of genes related to oxidoreductase (left) or cell wall (right) functions that were upregulated in RG1.9, classified as in panel B. Annotations with SLIV/ SCO gene IDs are indicated. Asterisks: genes that belong to the SigR or SigE regulons