Fig. 2: FOXK1 promotes the expression of E2F target genes.

a MA Plot representing the mean expression against the fold change of genes when comparing FOXK1 with empty vector or FOXK1 with FOXK2 conditions. For each graph, genes in red are up-regulated in FOXK1 condition. b Gene ontology (GO) analysis using Enrichr (MSigDB and GO:BP databases) was performed on genes differentially regulated between FOXK1 and FOXK2 conditions. c Gene set enrichment analysis (GSEA) performed on genes deregulated in FOXK1 compared to FOXK2 condition. d Heatmap representing the transcript count in IMR90 cells from control, FOXK1 and FOXK2 conditions on all the E2F target genes defined by the hallmark of molecular signatures database (200 genes). Among the 200 E2F genes, FOXK1 upregulates 60 of them. Transcript counts were normalized using z-score and presented as heatmap. e Validation of RNA-seq data by quantifying mRNA of genes differentially regulated by qRT-PCR (n = 4 independent experiments). f Western blotting showing increased expression of some E2F targets following FOXK1 or FOXK2 overexpression (representative of three independent experiments). g IMR90 cells expressing FOXK1 or control cells were treated with the CDK4/6 inhibitor Palbociclib (5 µM) and monitored for growth using Incucyte imaging (n = 3 independent experiments). h Kaplan–Meier survival curve of TCGA cancer patients with or without FOXK1 amplification (based on GISTIC score) with separate analysis for male (number of patients without amplification = 3043, and with amplification = 49) and female patients (number of patients without amplification = 2500, and with amplification = 67) (data sourced from cBioportal). i Heat map showing z-scores of transcript counts for 200 E2F target genes, categorized into samples with the highest (top 10%) and lowest (bottom 10%) FOXK1 expression levels from TCGA cancer patients with separate analysis for male and female patients. j GSEA analysis conducted on differentially expressed genes when comparing TCGA samples with the highest and lowest FOXK1 expression levels. Statistics: Data are represented as mean ± SEM (e, g). Two-way ANOVA with two-sided tests followed by Dunnett’s multiple comparisons test for adjustment (e, g). Normalized enrichment score (NES) and p value were computed using GSEA software (c, j). A two-sided log-rank test was performed for survival analysis (h). *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.001, ns non-significant. Source data are provided as a Source Data file.