Fig. 4: Differential expression during craniofacial development.
a Heatmap of differentially expressed genes (log2 fold change > abs(1), Benjamini–Hochberg p-adj <0.05) across all samples in our developmental series. Z-scores for normalized gene counts ranging from high (yellow) to low (blue) expression. The dendrogram on the top is the hierarchical clustering of all samples. Samples were separated into two main clusters, Early (CNCC, CS13, and CS14) and Late (CS15, CS17, and CS22). The dendrogram on the left is hierarchical clustering of gene counts. The genes were assigned groups identified by color and number (1-dark green, 2-light green, 3-light purple, and 4-dark purple) by cutting the dendrogram at a height that would result in four clusters. The genes in the green clusters are those primarily expressed in the early and intermediate stages of the series. While the purple cluster genes tend to be active in the late stages. b Gene ontology of a select subset of the most significant terms identified by clusterProfiler146 for 2-light green and 4-dark purple clusters. The genes of the 2-light green cluster enrich for embryonic patterning and terms concerning the mesenchyme. The 4-dark purple cluster includes muscle developmental functions with ossification and blood vessel morphogenesis. c Network plot of selected significant disease ontology terms from genes of the 2-light green cluster. Count refers to the number of genes within a category and the colorbar shows log2 fold change as calculated by DESeq2141 between CS13 and CS17 samples which color the gene nodes.
