Figure 3

Seed coexpression network topology. (a) The Arabidopsis germination coexpression network. Outlined in yellow are defined regions in the network: region 1 represents clusters of genes associated with nongermination/dormancy; region 2 represents a transition from nongerminating/dormancy to germinating states; region 3 is associated with germination. Subnetworks generated from salt responsive transripts expressed in genotypes (b) TN1.13 and (c) TN1.15. (d) Subnetwork of overlapping salt responsive genes of TN1.13 and TN1.15. The red and blue nodes represent transcripts significantly associated with the upregulation of dormancy and germination, respectively. Yellow nodes in the subnetworks of (b) and (c) highlight genes of highly clustered modules. Reference Additional file 5 for node names and gene relationships of the highly clustered modules in (b.) and (c.).