Fig. 7

The relationship of 871 core hub genes to msh1-derived states and biologically meaningful core networks. a Venn diagram of Arabidopsis DMGs identified from four different msh1-derived states (Col-0 genetic background): msh1 mutant (state 1), msh1 memory (state 2), graft progeny (HEG, state 3), and epi-line (Epi 24, state 4). b An overview of the PPI networks and individual 871 core hub genes. Blue represents DMGs, orange represents the DMGs that are dcl2/dcl3/dcl4-sensitive in graft progeny contrasting mutant rootstock analyses. c Hierarchical clustering of individual plant datasets from four different msh1-derived states based on the sum of Bayesian methylation level difference of DMPs over the 871 core genes from panel a. The hierarchical clustering was built using Ward agglomeration method. The Bayesian methylation level difference was computed as described previously [18]. d Main subnetwork of hubs obtained with the application of a machine learning k-means clustering algorithm on the set of 871 core genes from panel a. 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. In total, 67 genes involved in enriched networks were identified. Blue nodes represent DMGs, with orange representing the DMGs that are dcl2/dcl3/dcl4-dependent in graft progeny contrasting mutant rootstock analysis. This 67-gene set supplied the RdDM candidate target genes for further study. Blue gene text represents DMGs proximal to only TE sequences, red text designates genes that are proximal to only sRNA clusters, and black text represents genes proximal to both TE and sRNA clusters. For both b and d, the size of each node is proportional to its value of node degree and the label font size is proportional to its betweenness centrality