AP2a binding sites having the highest score computed from the weight matrix prediction algorithm were AbMole Ellipticine localized on the DNA sequences imobilized on the PBM, and the corresponding genomic sequences were assayed for AP2a-interaction by chromatin AbMole Pyriproxyfen immunoprecipitation-quantitative PCR using a colon cancer cell line that constitutively expresses this transcription factor. AP2a was indeed found to interact with the predicted sites on the GAS2 and on KLK-5 upstream regulatory sequences in the cancer cells as well as to the AP2a binding site in the promoter of the estrogene receptor gene used as a positive control. RNA polymerase II was found to bind to the KLK5 promoter but not to that of GAS2, as expected from the activating and repressive role of AP2a seen in transfection studies, respectively. This indicated that the PBM and in silico analysis allowed the identification of functionally relevant target genes. It has been proposed that AP2a DNA-binding specificity is modulated by synergistic or antagonistic interactions with other DNA binding proteins present in human tumor cells, and that changes in these interactions may lead to tumor progression. AP2a association was therefore also assessed on the 6000 human genomic regulatory sequences in conditions where these competitive or synergistic interactions may take place. Nuclear extracts were generated from 4 healthy breast tissues and 8 breast cancer biopsies, and they were applied to hu6k microarrays to specifically detect AP2a binding. Among the 998 target sequences obtained from both the healthy breast tissue and the breast cancer protein extracts using the log fold change as endpoint, 53 also associated with the purified protein. These likely corresponds to direct binding targets of AP2a as exemplified by chorionic gonadotropin alpha promoter, which is a well characterized functional and binding target of AP2a in tumor cells. The synergistic or antagonistic binding of AP2a with numerous other DNA-binding proteins may explain different gene occurrence in the various datasets. For instance, interactions observed from nuclear extracts of healthy and/or cancerous tissues, but not from purified AP2a may result from its ability to piggy-back other DNA-binding proteins such as YY1, Sp1 or p53. Using a position weight matrix prediction algorithm for AP2a binding sites, we tested the 50 sequences most prominently bound by AP2 from the PBM data sets generated with recombinant AP2a and with the normal and tumor tissue extracts. We found that the occurrence of AP2a predicted binding sites was 1.5 fold lower in sequences obtained using normal tissue extracts as compared to those obtained with the recombinant AP2a. This result thus supports the interpretation of an indirect binding of AP2a occurring from tissues extract and the proposed ability of AP2a to interact with other proteins to bind its target genes in the context of normal cells.