Fig. 2: Conserved and divergent network connections between tassel and leaf gene regulatory networks.
From: Regulatory variation controlling architectural pleiotropy in maize
a Gene co-expression network (GCN) preservation between “tassel” and “leaf” networks defined from a permutation test (n = 1000 permutations). One-sided p values are determined from the Z-score of individual measures under the assumption of normality. Preserved modules are indicated by color and connected by lines (width is proportional to number of preserved genes). Colored boxes beneath the plot represent examples of preserved gene co-expression sub-modules. b Topological graph representation of preserved TFs in the “tassel”-“leaf” “brown-green” sub-module based on data from GCN (edge weight) and gene regulatory network (GRN; edge directionality). Pink edges represent preserved regulatory connections, and brown or green edges represent the network-specific wires. c Topological graph representation of closest TF neighbors to liguleless2 (lg2) in the ‘tassel’ and ‘leaf’ networks based on data from GCN (edge weight) and GRN (edge directionality). Pink edges represent preserved connections (pe preserved edges), and blue or brown/green edges represent network-specific wires (npe non-preserved edges). The edge length is proportional to the weight of gene co-expression. Nodes are colored based on their GCN module designation. Maize gene labels are from MaizeGDB or AGPv4 as Zm00001d(6). Source data are provided as a Source Data file.
