Table 1 Summary of potential new candidate genes for nsCL/P based on different analysis approaches.

From: Combining genetic and single-cell expression data reveals cell types and novel candidate genes for orofacial clefting

Analysis approach

Prioritized nsCL/P candidate genes

scDRS TAD gene

RPL35A, C10orf82, MSX1, GADD45B, ARHGAP29, TLE2, NSD3, TIMM13, RAB11FIP1, NBL1

scDRS gene

KRT19, CLDN6, EPCAM, CLDN4, CLDN7, RAB25, RPS14, RPL41, RPS18, AP1M2

hdWGCNA + GWAS

CTNND1, PRTG, BFAR, HYAL2

DEGs

ARHGAP29, MYC, GADD45B, RAB11FIP1, PLKHF2, NSG1

  1. The top 10 genes per analysis approach are shown, the remaining genes for scDRS TAD gene and scDRS gene are listed in table S5. Genes that have not been previously reported with nsCL/P are shown in bold.
  2. Analysis approaches are defined in the main text.
  3. Abbreviations: Differentially expressed genes (DEGs), genome-wide association study (GWAS), high-dimensional weighted correlation network analysis (hdWGCNA), non-syndromic cleft lip with or without cleft palate (nsCL/P), single-cell disease relevance score (scDRS), topologically associating domain (TAD).
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