To identify the molecular events which occur in response to HDAC inhibition in colon cancer cells, we treated both HCT116 and HT29 colon cancer cells with the clinically relevant concentrations of 50 nM LBH589 or 2 μM vorinostat for 24 h, isolated mRNA and subsequently analyzed gene expression using the Illumina Human-6 V2 BeadChip array platform as outlined in the methods section. Here, HDAC9 is linked to malignant colon neoplasm.