Fig. 4

The CTNND2 module is altered in the epithelial cells of EAC and Barrett’s Esophagus. a Barplot displaying the number of differentially methylated genes (DMG), and the subset of these that are specifically differentially methylated in the epithelial (Epi), fibroblast (Fib) and immune cells (IC) for each of the 12 EAC FEM-modules, as determined in the EAC TCGA DNAm dataset. b tSNE diagrams for the 2009 epithelial single cells profiled in samples derived from 4 patients diagnosed with BE. The first panel displays the inferred 6 clusters. The middle panel labels the cells by the site of sampling (tissue): BE = Barrett’s Esophagus, DuoD = duodenum, Gastric = gastroesophageal junction, Oesoph = adjacent normal squamous cells from oesophagus. The right panel labels the cells by the patient they derived from. The Chi-Square statistics and associated P values were derived from a contingency table test, assessing how unevenly tissue and patient are distributed among the inferred clusters. c Violin plots displaying the FEM cancer-score for the CTNND2 module in a scRNA-Seq dataset comparing epithelial cells from Barrett’s Esophagus lesions (BE) to adjacent normal squamous epithelial cells for each of 4 different patients diagnosed with BE. Last panel is for the case where all cells from all patients are merged. P values are from a one-tailed Wilcoxon rank sum test