Fig. 3.
β-Catenin uses Tcf-1 to down-regulate replication, HR repair, and checkpoint control pathway genes. (A) Spearman correlation of differentially expressed genes (P < 0.05) between CAT and either Cre or CAT-Tcf7Δ. (B) Pathway analysis of restored DEGs that were up-regulated (red) or down-regulated (DN, blue) in CAT versus Cre and CAT-Tcf7Δ (Metascape, www.metascape.org). (C) Unsupervised clustering of triplicate RNA-seq profiles (FPKMs) for Cre (n = 3), CAT (n = 3), and CAT-Tcf7Δ (n = 3) DP (CD4+CD8+) thymocytes; gene clusters associated with altered expression in CAT thymocytes that are restored to Cre levels in CAT-Tcf7Δ are shown. (D) Functional pathways enriched in cluster 1 and cluster 6 gene sets (Metascape). (E) GSEA/MSigDB of cluster 1 gene expression showing significant signatures (normalized enrichment score (NES) > 1 Faulse Discovery Rate (FDR) < 0.2) with relevant genome maintenance programs labeled and highlighted in red. (F) Representative GSEA profiles and (G) heatmaps of core enrichment genes of the indicated pathways; central replication and repair genes are highlighted (red).