Figure 2

Clustering and functional categories of significantly regulated genes. A) Cluster analysis (Genesis, see Methods) of data from individual experiments. The log₁₀ values for each microarray signal divided by the corresponding average control (Tv) signal are plotted in the heat map, clustered by relative expression level and experiment. B) A portion of the cluster analysis, annotated by protein ID number. This magnified portion of (A) shows a cluster of genes up-regulated in response to both maize and tomato roots. Yellow dots indicate 7 of the 14 genes significantly up-regulated in response to both plant hosts (C). C) Expression patterns of genes significantly up-regulated in response to both plant hosts. Patterns are plotted for the 14 genes identified by CyberT analysis. D) Pie chart of functional categories for the set of genes shown in A. For simplicity large categories were used; the “metabolism” category includes, for example, a large number of predicted proteins with reductase, dehydrogenase, and other enzymatic activities, as well as some secreted hydrolytic enzymes with the exception of glycoside hydrolases which are listed separately. See Additional file 3: Table S2 for the complete annotated list.