Bacterial artificial chromosomes (BACs) constitute minimal components of various whole genome-sequencing projects, including our own. The recent innovation of efficient recombinogenic bacterial strains allows systematic BAC modifications (i.e. recombineering; Reviewed in Copeland et al., 2001), setting BACs as an ideal experimental basis for functional genomics with their broad coverage of transcriptional regulatory elements. For instance, in the field of neuroscience, the GENSAT project extensively modified mouse BAC clones, covering gene transcriptional units preferentially expressed in the nervous system, and generated hundreds of BAC transgenic (Tg) mouse lines from those modified BACs (Gong et al., 2003). These BAC-Tg lines successfully recapitulated complex gene expression profiles in the nervous system (Gong et al., 2003), providing a rigid analytical platform so as to be able to answer the fundamental question of how tens of millions of neurons and thousands of cell-types can become elaborate interconnected circuitries in the brain by using only twenty-thousand sets of gene transcriptional activities.