Outline of the procedure for comparing tissue- and/or genotype-dependent metabolomic correlations in Arabidopsis. Three genotypes [methionine-over accumulation 1 (mto1), transparent testa4 (tt4), and wild-type (WT)] were studied. Samples from aerial parts and roots were analyzed by GC-TOF/MS-based metabolite profiling and changes in mean metabolite levels were assessed and calculated by multivariate statistical analysis PCA, the rank product method, and the metabolomic correlations by the Spearman correlation coefficient. Then we constructed the metabolomic correlation networks. Using DPClus  we extracted densely connected metabolites. Lastly, we characterized each cluster based on the KEGG enrichment analysis to assess statistical significance.