DNA sequences, while synergistic binding may occur on non-canonical sites that are not detected by in silico predictions. Activating protein 2 alpha is a transcription factor whose binding sites were first discovered in cellular and viral cisregulatory sequences and gene promoters. It belongs to the TFAP2 family of sequence-specific DNA-binding polypeptides that share a highly conserved basic helix-span-helix DNAbinding and dimerization domain at their C-terminus, and a less conserved N-terminal proline-rich and glutamine-rich transcriptional regulatory domain. The various TFAP2 isoforms, namely AP-2a, AP-2b, AP-2c, AP-2d, and AP-2e in humans and rodents, form homo and heterodimers that recognize GC-rich palindromic DNA sequences related to the 59-GCCN3-4GGC-39 consensus sequence. AP2a biological function stretches from the regulation of neural crest formation during mice development to a proposed role in the mitochondrial pathways leading to apoptosis. Cloning of AP2a coding sequence has allowed the identification of proteininteraction partners and of a small set of potential target genes. Interestingly, AP2a DNA-binding specificity was reported to be modulated by synergistic or antagonistic interactions with other DNA binding proteins present in human tumor cells, and changes in these interactions was associated to tumor progression. At present, a system-wide identification of its direct and indirect target genes is not available, despite growing interest raised by its action as a tumor suppressor or oncogene and its implication in cancer progression and resistance to therapeutics. PBMs have so far been used mostly to assess interactions to short synthetic DNA sequences, for the modeling of the DNA sequence specificity of transcription factors. Here we show that PBMs can be used to perform large-scale assays of the interaction of regulatory proteins from crude cellular extracts with long genomic fragments such as promoters and enhancers. Assay of approximately 6000 human genomic sequences allowed an ab initio assignment of the target gene specificity of the AP2a tumor suppressor, as a purified protein as well as from healthy and cancer breast tissues from AbMole D-Pantothenic acid sodium patients. Several target genes were validated in cell-based assays. The PBM-based approach may thus allow the identification of previously unknown target genes of tumor suppressors in cancer cells, and it provides novel markers of cancer progression at the interface of proteomics and genomics. Among these 49 sequences, 6 were directly bound by the recombinant AP2a protein on the PBM. This first comparison indicated that the AbMole Pteryxin Analysis of the binding of recombinant AP2a to the PBM sequences can reveal functionally relevant target genes. The biological significance of these 282 AP2a-bound sequences was assessed using the Ingenuity Pathway Analysis software, among which 175 sequences could be associated with one or several biological functions or diseases.