Figure 5

Weighted gene co-expression network construction and analysis for CLCuD-responsive cotton genes in CLCuD symptomatic and asymptomatic leaves. (A) Transcriptomic data from symptomatic and asymptomatic leaves was analyzed by WGCNA using 468 DEGs. Genes were clustered as per expression arrangements characterized by the dendrogram and topological overlap mapping metric (TOM) heat map. Each line of the dendrogram corresponds to a gene. Clusters of similarly-regulated genes are grouped as modules by corresponding color (blue and turquoise) with a threshold minimum module size of 70 genes. The intensity of pink coloring in heatmap specifies high strength and green as no strength of correlation between pairs of genes on a direct scale and features hierarchical clustering dendrograms possessing a range of weighted correlations. (B) Weighted network illustrates correlations (edges) among the nodes (genes) with a weighted correlation threshold of ≥0.85. The network is composed of 468 connections and 348 genes organized in two different modules. The node color corresponds to modules identified via WGCNA. Nodes with high connectivity ( ≥5 connections, hubs) among different modules are indicated with increased node size. (C) Highly connected nodes (hubs) within the co-expression network are shown. Average degree of turquoise and blue modules is not changed in the entire co-expression network (2.689655172). (D) Clustering coefficient (degree to which a node is connected in a neighborhood) for genes within each node is illustrated in a box plot. Turquoise module displays significantly a higher average clustering coefficient than whole co-expression network (0.443746579). (E) The information centrality (the flow of information between any two nodes in a connected network) for the largest component of co-expression network (92 nodes) is presented. Turquoise module displays significantly increased information centrality compared to the entire network (0.005299235). (F) Interactive graph of GO terms associated with cotton leaf curl disease responsive G. arboreum hub genes identified by co-expression network analysis. Analysis performed with online tool agriGO (bioinfo.cau.edu.cn/agriGO/) where a key indicates significance levels of GO terms.