Figure 2.

Computationally predicted differentially expressed genes.A) Symptomatic vs. mock comparison revealed a total of 254 differentially expressed genes, of which 147 were up-regulated and 107 down-regulated. A comparison of recovered vs. mock comparison revealed 264 differentially expressed genes, of which 145 were up-regulated and 119 were down-regulated. When symptomatic and recovered tissues were compared, only 2 genes were up-regulated in the recovered relative to symptomatic tissue. B) Hierarchical clustering of genes identified as differentially expressed in PepGMV-infected pepper plants. Log2 expression values were used for the analysis and negative values were set to zero. Clustering and the heat map were performed using R [71]. Green indicates down-regulated, red up-regulated and black unchanged values, as shown on the color scale at the side of the figure. C) Principal component analysis of differentially expressed genes. The percentage of variance explained by each component is shown within the brackets. R/S = Recovered vs. Symptomatic, S/M = Symptomatic vs. Mock and R/M = Recovered vs. Mock. D) Comparisons between S/M and R/M show that nearly 80% of differentially expressed genes are identical to both comparisons; 124 up-regulated (red) and 85 down-regulated (green) genes are differentially expressed in symptomatic and recovered tissues vs. mock-inoculated.

G√≥ngora-Castillo et al. Virology Journal 2012 9:295   doi:10.1186/1743-422X-9-295
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