TABLE 1.

CL/P candidate genes with specific expression in Irf6+ facial epithelial cells.¹ adjusted p-value (based on Bonferroni correction using all genes in the data set);² average log₂ fold change in the average expression between the two tested groups (second test group: all other cell types; positive values indicate that the gene is more highly expressed in the respective cell type compared to all other cell types). NsCLO (non-syndromic cleft lip only).

Cell type	Gene	P-val. adj.1	Log2FC2	Cleft association in humans
Periderm	Tpm1	1.9E-09	1.08	nsCL/P GWAS (Ludwig et al., 2012)
	Pik3r1	6.1E-10	0.75	nsCL/P GWAS (Leslie et al., 2017)
	Tfap2a	4.9E-44	1.03	Branchio-oculo-facial syndrome (Milunsky et al., 2008), nsCL/P GWAS (Ludwig et al., 2012; Leslie et al., 2017)
	Wnt3	1.0E-10	0.25	Tetra-amelia syndrome 1 (Niemann et al., 2004)
	Ctnnd1	0.0002	0.42	Blepharocheilodontic syndrome 2 (Ghoumid et al., 2017)
	Fras1	8.0E-10	0.69	Fraser syndrome (Fraser, 1962)
Basal cells at fusion zone	Spry2	4.0E-37	1.29	nsCL/P GWAS (Ludwig et al., 2012)
Ectodermal surface	Arid3b	7.7E-13	0.3	nsCL/P GWAS (Leslie et al., 2017)
	Zfp36l2	0.008	0.26	nsCL/P (Lin-Shiao et al., 2019), nsCLO (Li et al., 2022)
Ectodermal surface (Robo2+)	Tpm1	0.04	0.3	nsCL/P GWAS (Ludwig et al., 2012)
Palatal epithelium	Cyb561	1.6E-36	0.3	nsCL/P GWAS (Leslie et al., 2016)
	Ptch1	0.0001	0.33	nsCL/P GWAS (Yu et al., 2017), CPO GWAS (Butali et al., 2019), Basal cell nervous syndrome (Evans et al., 1993; Kimonis et al., 1997; Kimonis et al., 2013)
	Tfap2a	1.9E-09	0.27	Branchio-oculo-facial syndrome (Milunsky et al., 2008), nsCL/P GWAS (Ludwig et al., 2012; Leslie et al., 2017)
	Fras1	2.0E-08	0.33	Fraser syndrome (Fraser, 1962)
	Ripk4	5.3E-32	0.3	Popliteal pterygium syndrome, Bartsocas-Papas type 1 (Bartsocas and Papas, 1972)
Olfactory epithelium	Arid3b	2.5E-11	0.25	nsCL/P GWAS (Leslie et al., 2017)
	Cyb561	5.0E-55	0.29	nsCL/P GWAS (Leslie et al., 2016)
	Xpa	0.0003	0.26	nsCL/P GWAS (Welzenbach et al., 2021)