Fig. 4: Unsupervised gene co-expression networks recover shared programs.
From: Time-resolved oxidative signal convergence across the algae–embryophyte divide
WGCNA was used to compute co-expression networks. a Distance dendograms of module correlation with metabolites, condition, and photophysiology. b Heatmaps of module trait correlation with metabolites, condition, and photophysiology corresponding to the distance trees in a. c Scaled Jaccard distances that illustrate similarity (pink) and dissimilarity (blue) between modules based on HOGs. d The 50 most similar modules; GO terms enriched among pairwise similar clusters are shown in Supplementary Fig. 18. e cnetplot of the GO terms enriched in the cluster Mebrown. f–j Selected WGCNA clusters with the top 20 most connected genes (the hubs) annotated based on homology; next to the clusters, the total number of genes within the cluster is noted in colored font (see also Supplementary Data 2). k Selection of GO terms enriched in clusters defined by WGCNA in Zygnema circumcarinatum, Physcomitrium patens and Mesotaenium endlicherianum presented as biological theme comparison; for the whole plot, see Supplementary Fig. 4. l Quantification of the shared occurrence of all 1860 top20 hubs (in 1473 HOGs) in all three species based on orthogroups assignment. All networks can be explored interactively at at https://rshiny.gwdg.de/apps/streptotime.
