Fig. 4

Gene ontology (GO) term enrichment studies and gene over-representation analyses (ORAs) to identify cellular consequences of PALS1 depletion in MDCK cells. FLOW chart: The individual transcriptomes from non-confluent and 3D cell cultures of WT and PALS1 KO MDCK cells were first processed and grouped using DEseq2. Subsequently, various comparisons were conducted to obtain contrasts called subset A, B, C, and D, respectively (green box). Only genes that were at least a 2-fold up- or downregulated and adj. P < 0.05 (cut-off criterion) were considered. Up- and down-regulated DEGs were then utilized for gene ontology (GO) enrichment studies (category: BP from Biological Process) or gene over-representation analyses (ORAs). Here, predominantly pathways with adjusted p-values P < 0.05 were considered (cut-off criterion). The top 30 significant pathways (TOP30) in each case were further evaluated