Fig. 1: ATF4 governs gene expression in a signal-dependent manner.

a–c RNA-seq was conducted on the HMLE cells transduced with a scramble shRNA (shCtrl) or an ATF4-targeted shRNA (shATF4) and treated with indicated conditions (Twist-OE, Twist overexpression; Tg, thapsigargin). a A heatmap showing the expression of genes that were downregulated by ATF4 knockdown and ranked in the top 2.5% under Twist-OE or Tg treatment, respectively. b GO (gene ontology) enrichment analysis for genes downregulated by ATF4 knockdown for more than 1.5-fold in Tg treatment. A list of top enriched genesets (upper panel) and a GSEA (gene set enrichment analysis) plot showing the enrichment of the unfolded protein response pathway (lower panel) were shown. Hypergeometric test was used to identify significant enrichment pathways (P < 0.01). The statistical significance (nominal P value) of the normalized enrichment score (NES) was generated by employing an empirical phenotype-based permutation test. c GO enrichment analysis for genes downregulated by ATF4 knockdown for more than 1.5-fold when Twist was induced. A list of top enriched genesets (upper panel) and a GSEA plot showing the enrichment of the epithelial-mesenchymal transition pathway (lower panel) were shown. Hypergeometric test was used to identify significant enrichment pathways (P < 0.01). The statistical significance (nominal P value) of the normalized enrichment score (NES) was generated by employing an empirical phenotype-based permutation test procedure. d–f RNA-seq was conducted on the LX-2 cells transduced with a scramble shRNA (shCtrl) or an ATF4-targeted shRNA (shATF4) and treated with indicated conditions. Similar analyses were conducted as in (a–c). Hypergeometric distribution tests were applied for GO enrichment analysis and weighted Kolmogorov–Smirnov tests were applied for GSEA. These analyses were conducted on the average data of two biological replicates.