Fig. 2: Multiple cluster analysis of metabolites and genes.

a Workflow of the gene-metabolite cluster analysis. b Mapping relationship of different clustering between two methods. Pink lines represent some known metabolic associated genes. c Characterization of the final clustering. The word cloud shows the TF family enrichment analysis. Font size represents the -log (FDR). Blue lines in each cluster display the average metabolite content or gene expression level. d Pearson correlation coefficients (PCCs) and GINI coefficients between same cluster (purple) and random (green) gene-gene or gene-metabolite pairs. e Significant overlap of regulatory pairs identified through distinct methodologies indicates the robustness of regulatory relationships. f Ternary plot shows the deviation in the distribution of correlations between metabolites (ME) and structural genes (SG), transcription factors (TF) and MEs. g PCCs and GINI coefficients between metabolites is significantly higher than that between metabolites and SG or TF. Blue lines represent the median values. Different lowercase letters indicate significant differences (PCCs: a vs b P = 2.18e-16, b vs c P = 3.87e-17, a vs c P = 5.87e-22; GINI: a vs b P = 3.52e-17, b vs c P = 4.77e-18, a vs c P = 6.3e-25). A two-tailed Games Howell test was used to determine P values. h PCCs and GINI coefficients between the expression values of the known metabolic associated TFs and those of their targets in the same cluster (n = 4 biological replicates). Error bars represent the means ± standard errors of four biological replicate. i PCC correlation between dihydroactinidiolide (DHA) and expression level of SGs. j PCC correlation between NtLOX2 and expression level of TFs. k PCC correlation between chlorogenic acid (CGA) and expression level of SGs. l PCC correlation between Nt4CL2A, NtPAL2 and expression level of TFs. m GINI correlation between DHA and expression level of SGs. n GINI correlation between NtLOX2 and expression level of TFs. o GINI correlation between CGA and expression level of SGs. p GINI correlation between Nt4CL2A, NtPAL2 and expression level of TFs. In (c) and (e), The P values were calculated using hypergeometric distribution (two-sided) and then adjusted using the FDR. Source data are provided as a Source Data file.