Fig. 6
From: Methylome decoding of RdDM-mediated reprogramming effects in the Arabidopsis MSH1 system
PPI hubs derived from subsets of network-related DMGs and DEGs in Epi 8 and Epi 24. Epi 8 and Epi 24 represent progeny lines derived from the same cross, with Epi 8 displaying enhanced vegetative growth rate and Epi 24 significantly enhanced seed yield. The main subnetwork of hubs was obtained with the application of machine learning k-means clustering on the set of 3647 (Epi 8, panel a) and 3523 (Epi 24, panel b) network-related DMGs and DEGs (p < 0.1) identified in the Arabidopsis epi-line vs WT comparison. The analyses yielded 153 (a) and 346 (b) hub genes to form a closely related subnetwork. GO network enrichment analysis from the string application in Cytoscape [27] was used to identify enriched gene function pathways (FDR < 0.05) within the network. Blue represents DMGs, green represents DEGs, and magenta represents both DMGs and DEGs. Size of each node is proportional to its value of node degree and label font size is proportional to its betweenness centrality