Clustering of the stress-annotated, pathogen-responsive genes in the 351-gene-set. Hierarchical clustering was represented for the 43 gene-entities using Euclidean distances and following Ward’s Linkage rule. Branch A1 includes genes that are activated upon pathogen challenge and repressed in NP-exposed plants. This branch contains most SAR-responsive genes. Branch A2 corresponds to genes activated by pathogen challenge and also, but to a lesser extent, by NP exposure. Branch B is formed by the genes repressed both by pathogen and NP-exposure (box-plot representations for each branch in Additional file 5).