Supplemental Dataset 6

Supplemental Data. Walker et al. (2017). Plant Cell 10.1105/tpc.16.00961. Supplemental Dataset 6. Network statistics and module annotation and characteristics .(A) For each causal regulatory network 8 statistics are shown: number of edges, number of nodes, the node/edge ratio, number of connected TFs, number of targets of those TFs (including TFs that are targets), average targets per TF, the network clustering coefficient and the characteristic path length as given in Cytoscape. (B) Comparison of TF module size and timing response category for CN and PN networks. (C) Network statistics for major modules in each experiment are shown with a cut off of >=10 targets in at least one experiment. The status of each TF in the network in each experiment is shown (DE (0 not DE, 1 DE), indegree, outdegree). The combined outdegree is the sum of the shown out degrees across the six experiments, the number of experiments where outdegree is >7 is also shown. Maximum module size was in part dictated by the number of genes in the network, while the mean number of targets per TF was larger in CU and CN. This indicates that the pericycle and cortex networks have statistically different structures and this was confirmed by analysis of the network connectivity using size independent statistics; specifically there were differing levels of clustering, CN was the least clustered whereas PN had the longest path length while still being highly clustered. This indicates that the cortex is dominated by a few large modules, while the pericycle is more distributed amongst a larger number of modules, in fact extending to very large sizes. (D) Corroborated interactions based on the presence of cis-acting TF family binding sites for networks. Data derived from Franco-Zorrilla et al 2014 [83]. Source contains TFs that interact with a putative regulated gene (Target) and the type of interaction (activation/inhibition) is shown.