In this study, we evaluated whether double-stranded DNA fragments bearing whole promoters and regulatory sequences and immobilized on a PBM may be used to identify the target genes of an oncogenic transcription factor. We found that binding values obtained from the PBM correlated well with the affinities determined by surface plasmon resonance or computed with a weight matrix. This indicated that PBMs provide reliable estimations of the binding strength. Genomic fragments that bind AP2a on the PBM and/or in silico were found to mediate AP2aregulated expression in transfection assays. Occupancy of the AP2a binding sites within the native chromatin structure of tumor cell lines was confirmed experimentally. This also indicated that valid target genes may be identified by combining these PBM and modeling approaches. Thus, the increase in non-specific background binding to the long DNA molecules, as resulting from the use of relatively long promoter and enhancer sequences, did not mask sequence-specific functional interactions. In vivo, an additional level of complexity arises from the chromatin structure, which may shield the DNA from protein binding. Thus, a high binding potential in vitro or in silico cannot provide definitive evidence that a putative binding site will be occupied in any given cell type. Furthermore, binding may be occluded by other transcription factors that interact with overlapping sites on the promoter, or conversely, protein association may allow interactions to non-canonical sites. The relative contributions of chromatin and of other transcription factors to the actual binding site occupancy in vivo remains difficult to assess for eukaryotic transcription factors, as large-scale assays of promoter binding occupancy with chromatin alone, or with competing or synergizing transcription factors but without chromatin, have not been available. The finding that the most prominent functional feature of AP2a target genes relates to cancer was validated experimentally for two newly identified AP2a target genes. Kallikrein 5 is a member of the kallikrein family of extracellular Gefitinib msds proteases that includes the prostate-specific antigen, and it is currently emerging as some of the most prominent biomarkers of tumor progression for various types of cancers. The growth-arrest specific 2 protein modulates cell susceptibility to p53-dependent apoptosis upon chemotherapy. The finding of an BU 4061T AP2a-mediated regulation of both genes may thus provide a molecular mechanism for its proposed role in tumor progression and resistance to chemotherapy.