The ATM protein, which is mutated in the inherited disease ataxia telangiectasia (AT), is a key regulator of the cells' DNA damage response. AT cells also exhibit constitutive activation of transcriptional regulators such as p53, E2F, AP1, and NFkappaB. Inactivation of ATM may therefore alter the cells' transcriptional profile. ATM expression in HeLa cells was silenced with siRNA expressed from a plasmid based vector, generating a stable cell line, HeLaATM601. HeLaATM601 cells displayed minimal levels of ATM protein and had a 10-fold increase in sensitivity to ionizing radiation. DNA microarray analysis demonstrated that 35 genes were upregulated and five genes were downregulated in HeLaATM601 cells. Genes upregulated in the absence of ATM included interferon-response proteins, cell cycle regulators, integral membrane proteins, and adhesion and extracellular matrix proteins. Using real-time PCR, these genes were also upregulated in cells derived from AT patients. Inactivation of the ATM protein therefore has a significant impact on the transcriptional profile of the cell.