Fig. 3

Expression analyses of AP4-deficient adenomas from Apc^Min/+ mice. a Venn diagram displaying differentially regulated RNAs (fold change ⩾ 1.5, p < 0.05) in Ap4^fl/fl and Ap4^∆IEC Apc^Min/+ adenomas as determined by edgeR and DESeq2. b Volcano plot and heatmap depicting expression changes between Apc^Min/+/Ap4^fl/fl and Apc^Min/+/Ap4^∆IEC tumors from 120 days old mice derived from three female mice (five tumors per mouse) per genotype detected by RNA-Seq. Volcano plot: p-values are plotted against the log₂ of the corresponding RNA expression changes in Ap4^∆IEC versus Ap4^fl/fl adenomas. Differentially expressed RNAs (p-value < 0.05) with a log₂ fold change ≥ 0.58 are indicated in red, with a log₂ fold change ≤ −0.58 are marked in blue. RNAs with 0.58 > log₂ fold change > −0.58 and/or with a p-value ≥ 0.05 are represented by gray dots. Dashed vertical lines indicate cut-offs for differential expression. Dashed horizontal line indicates the cut-off for adjusted p-values < 0.05 as determined with DESeq2. c Heatmap depicting expression changes of differentially expressed mRNAs (fold change ⩾ 1.5 and p < 0.05 as determined by edgeR and DESeq2) as relative expression levels normalized to the mean expression in the control, Apc^Min/+/Ap4^fl/fl, samples for each indicated mRNA. Colors indicate relative expression values from minimum (blue) to maximum (red) for each RNA sample per differentially regulated mRNA. Three biological replicates per genotype were analyzed