Microarray expression profiles were obtained using the Affymetrix GeneChip Human Gene 1.0 ST Array (Affymetrix, Santa Clara, CA). Amplification, labelling and hybridizations were performed according to protocols from Ambion (Ambion/Applied Biosystems, Foster City, CA, USA) and Affymetrix (Affymetrix Inc.). Briefly, 200 ng of total RNA were amplified using the Ambion WT Expression Kit (Ambion/Applied Biosystems), labelled using the WT Terminal Labeling Kit (Affymetrix) and then hybridized to Human Gene 1.0 ST Array (Affymetrix) for 16 h at 45 °C and 60 r.p.m. in a GeneChip Hybridization Oven 640. Following hybridization, the array was washed and stained in the Affymetrix GeneChip Fluidics Station 450. The stained array was scanned using an Affymetrix GeneChip Scanner 3000 7 G, generating CEL files for each array. Normalized and log transformed gene expression values were filtered using a variance filter (σ/σ max) of 0.2. Each variable was standardized by subtraction of its mean value and division by its standard deviation across all samples. One p53KD-Ras/EGFR/SrciNPC outlier sample was removed from further analysis. Differential expression analysis was carried out using ANOVA in Qlucore Omics Explorer 2.3.
