Fig. 3

Co-expression gene modules of epithelium and HAND2+ PA. (a) Circos plot of nsCL/P genes in epithelial co-expression gene modules. The outer track shows the chromosomal cytoband, the inner track shows the positions of TADs described in Welzenbach et al. 2021³. The colors of the connecting lines correspond to the respective gene module. The strength of the connecting lines reflects the pairwise correlation coefficient between two genes multiplied by a factor of 30 for illustration purposes. (b) Circos plot of nsCL/P genes (black) and potential novel candidate genes (gray) in HAND2+ PA co-expression gene modules. Panel layout as described in a. (c) UMAP plots of epithelium (E-9, E-10, E-11) and HAND2+ PA (PA-12, PA-14, PA-15) colored according to the module eigengene values for each co-expression gene module. (d) Bar plots of selected GO terms for biological process (E-9 & PA-14) and molecular function (E-9) for the epithelial co-expression gene module E-9 and the HAND2+ PA co-expression gene module PA-14. The vertical dashed line is set at p-value -log₁₀ of 0.05. (e) Venn diagram of gene overlap between epithelial gene module E-9 and HAND2+ PA gene modules PA-12, PA-14, and PA-15. Epithelium (E), gene ontology (GO), non-syndromic cleft lip with/without cleft palate (nsCL/P), pharyngeal arches (PA), topologically associating domains (TADs).