A heatmap of over-represented categories from the metabolites versus genes correlation data. The level of representation of genes positively and negatively correlated with metabolites across all level of MapMan categories was subjected to cumulative hypergeometric distribution tests. Categories that are significantly enriched in positively correlated genes are colored in red (light red: 0.01 < P value < = 0.05; dark red: < P value < = 0.01); Categories that are significantly enriched in negatively correlated genes are colored in blue (light blue: 0.01 < P value < = 0.05; dark blue: < P value < = 0.01). For each category (rows) numbers in bracts are indicative of its level of classification (left) and the number of genes assigned to the category (left). (A) Categories at the top level of classification. Metabolites are ordered according to their classification pattern at the metabolites versus metabolites analysis (Figure 2B). Representative metabolites are marked in green. (B) Top over-represented categories across all MapMan classification levels. Five top categories were selected for each representative metabolite according to P values (Methods). Only over-representation of positively-correlated genes was considered. Metabolites are ordered consequently, according to their classification pattern at the metabolites versus metabolites analysis (Figure 2B). The full names of the metabolites are listed in Table 1. In order to simplify the visualization the original 97 categories were reduced into 83 by choosing single category to represent several similar categories (considering their higher level path) sharing the same enrichment profile across metabolites. E.g., a single category was chosen from the following categories at level 7: protein.synthesis.ribosomal-protein.prokaryotic.chloroplast.50S.subunit.L28; protein.synthesis.ribosomal-protein.prokaryotic.chloroplast.50S.subunit.L10; protein.synthesis.ribosomal-protein.prokaryotic.chloroplast.30S subunit.PSRP3; and protein.synthesis.ribosomal-protein.prokaryotic.chloroplast.50S subunit.L18 – all categories showing over-representation of genes positively correlated with pH.