The adenovirus E1A12S gene product (WT12S) immortalizes epithelial cells and they retain their differentiated characteristics, but certain mutants cannot do the latter. Characterization of mutant immortalized epithelial cells indicated that they had undergone epithelial mesenchymal transition (EMT). Coexpression of V12ras with WT12S leads to benign tumors, but to malignant tumors with 12S mutants. Since EMT is critical for tumor progression, identification of the molecular mechanisms involved should elucidate novel therapeutic targets. To this end, representational difference analysis (RDA) was used to identify cDNAs upregulated in the mutant cell line. Thirty-five differentially expressed mRNAs were identified and classified into several functional categories, including nine novel cDNAs. Among the 26 known cDNAs, extracellular matrix and related proteins made up the largest group of differentially expressed genes, followed by growth factors and receptors and transcription factors. There was also an ion transporter, a cytoskeletal protein, glycosylation and amidinotransferase enzymes and proteins with unknown functions. Some of the known genes have previously been associated with EMT and/or tumor progression and thus served to validate the system to obtain the desired target genes, while other cDNAs are newly linked with dedifferentiation/malignancy. Array analyses indicated that the cDNAs were specifically upregulated in invasive or metastatic tumors, especially of breast, uterus and lung, suggesting their involvement in the progression of these tumors.