Fig. 2

Target gene identification of the selected YAP enhancers. a Genomic views of the regions of the selected enhancers. The TAD (topologically associated domains) track represents a heatmap showing the frequency of chromatin interactions in 5 Kb bins in HMEC cells. The RNASeq/Ensembl track indicates known protein coding genes colored by the changes in gene expression (calculated as the average of log2 fold changes in gene expression between cells transduced with two different sgRNAs targeting the corresponding enhancer and non-targeting control sgRNAs). In gray are genes that did not significantly change. CTCF, ChIA-PET, and RNA Pol-II tracks were obtained from ENCODE from experiments performed with MCF7 cells using anti-CTCF and anti-RNA Pol-II, respectively (the color scales encode the number of reads supporting each interaction). b Heatmap plot showing the Pearson correlation coefficient between each selected enhancer target gene (a) and the YAP gene signature score in publicly available TCGA RNASeq samples from human tumors. The number in each tile represents the Pearson correlation coefficient in each TCGA study between the YAP gene signature score and the selected gene. The color scale represents the p value of correlation test, adjusted for multiple comparisons using Benjamini-Hochberg correction (ns, not significant; LowEx, low expression)