Skip to main content
. 2022 Jan 31;189(1):129–151. doi: 10.1093/plphys/kiac024

Figure 4.

Figure 4

BH t-SNE generated gene clusters and GCN analysis. A, BH t-SNE generated gene clusters based on their gene expression patterns. Total cluster (module) number was 48. Different colors indicate different clusters. B, The candidate genes that are included in the clusters are labeled with their corresponding colors. The selected gene clusters for GCN are labeled in yellow (CuRe1 and WRKY16 cluster, cluster 17), red (CCOMT and LAC cluster, cluster 11), blue (MYB55 cluster, cluster 39), pink (LIF1 cluster, cluster 46), green (CCR cluster, cluster 23) colors. CuRLR1 is in the noise cluster, and is labeled in gray color. Parameters used in this analysis: perplexity (perp) = 20, lying = 250, cutoff = 20, seed = 2. C–F, GCNs of four different Heinz susceptible and resistant cultivars upon C. campestris treatments. S indicates susceptible; R indicates resistant. Based on BH t-SNE analysis, 1,676 genes in cluster 11, 17, 23, 39, 46, and CuRLR1 were selected for building GCNs. +Cc indicates with C. campestris infection treatments. Different colors of the nodes indicate different modules based on GCN community structure. The genes that are listed at the left of the GCN and not labeled in the network are the genes that have no coexpression connections with all the other genes in the list.