Extended Data Fig. 7: Identification of key cCREs and TFs for distinct epithelial subtype.
From: A single-cell atlas of chromatin accessibility in mouse organogenesis
a, UMAP visualization showing the motif deviation scores (first row) and integrated gene expression (second row) of several cell-type or lineage-specific TF motifs in epithelial cells. b, TF footprints of Trp63 and Grhl1 motifs across 22 subtypes of epithelial cells. The Tn5 insertion bias track is shown below. c, X–Y plots showing the RNA expression levels (x-axis) and the transcription factor (TF) motif enrichment Z-scores (mean values) (y-axis) for several cell-type specific TFs. d, Heatmap summary of cCRE-to-gene links (n = 73,104) at 50 kb resolution where chromatin accessibility is highly correlated with target gene expression. Shown on the left are Z scores for scATAC-seq peak accessibility and on the right are Z scores for scRNA-seq expression. e, Bar plot of enriched gene ontology (GO) terms using genes whose number of linked cCREs was greater than 5 in epithelial cells. The y-axis indicates the GO terms; the x-axis indicates the adjusted P-value (one-sided hypergeometric distribution test). f, HOMER motif analysis of the top transcription factor motif enriched in stomach epithelium linked cCREs (n = 913), endocrine epithelium-linked cCREs (n = 706) and intestinal epithelium-linked cCREs (n = 808), detected using HOMER enrichment analysis with the one-sided hypergeometric distribution test with no adjustment for multiple-hypothesis testing. Source numerical data are provided as source data.
