Fig. 5: Developmental transcriptome organized into modules of coexpressed genes characterized by curated gene sets.

a Network plot of gene modules identified by WGCNA. A Pearson correlation of the module eigenvectors was calculated for the edges where positive correlations of ≥0.5 were included. The location of each module is determined by multidimensional scaling (MDS) of the module eigengene vectors. Modules are color-coded based on names assigned by WGCNA. The size of the dots indicates the number of genes in each module. Each module is labeled based on the most significant biological process category, gene ontology enrichment, determined by DAVID; however, this label is not always all-encompassing. See Supplementary Data 5 for an exhaustive list. Modules were grouped based on proximity and eigengene trajectory over developmental time. b Trajectories of expression based on eigengene vectors reported by WGCNA for each module across the developmental time series. The modules are assigned to one of three groups based on if it is generally decreasing, increasing, or oscillating over developmental time. See Supplementary Fig. 10 for all module trajectories. c Dot plots of gene list enrichment within the WGCNA modules. Gene lists (rows) are divided into four groups based on their source. Dec 1 through dec 3 are genes from these deciles, as reported by gnomAD. Disease gene lists from DisGeNET⁵⁶, CS craniosynostosis, CP cleft palate, CL cleft lip, CA craniofacial abnormalities. The rest of the lists are generated from data in this study. The dot color is determined by the Benjamini–Hochberg-adjusted permutation p value (see Methods), with darker indicating higher significance. Modules (columns) are grouped by their trajectory assignment from b.