Extended Data Fig. 10: Gene regulatory network validation against ChIP/DAP-seq data.
From: Integrated multi-omics framework of the plant response to jasmonic acid
a, The MYC2 subnetwork is shown. Edges are directional and red edges exist at early time points (0.25–2 h), blue only at late time points (4–24 h). Thicker edges with chevrons indicate that MYC2 were directly bound to that gene in our ChIP-seq experiments. b, Validated edges are those between TFs and first neighbors in the JA gene regulatory network for which the first neighbor was also a direct target of the TF in ChIP/DAP-seq assays. These edges are indicated by chevrons. Early time-series transcriptome-predicted edges (0.25–2 h) are red and later edges (4–24 h) are blue. Edges detected in the proteomic data are grey and those detected in the phosphoproteomic data are green. c, Bar plot shows quantification of JA-induced root growth inhibition in the indicated T-DNA alleles. Seedlings were grown on LS media with or without 20 µM MeJA. WT seedlings serve as independent controls for each tested T-DNA line. Sample size number n is shown within the respective bars. Samples are derived from three independent experiments. Asterisks represent significant differences between WT (-/ + JA) and indicated T-DNA lines (-/ + JA) (two-way ANOVA with Bonferroni post test, ns (not significant) p > 0.05, *p < 0.05, **p < 0.01, ***p < 0.001). d, Subnetwork of CYP708A2 is shown.
