The Allen Brain Atlas project (ABA) generated a genome-scale collection of gene-expression profiles using in-situ hybridization. These profiles were co-registered to the three-dimensional Allen Reference Atlas (ARA) of the adult mouse brain. A set of more than 4,000 such volumetric data are available for the full brain, at a resolution of 200 microns. These data are presented in a voxel-by-gene matrix. The ARA comes with several systems of annotation, hierarchical (40 cortical regions, 209 sub-cortical regions in the whole brain), or non-hierarchical (12 regions in the left hemisphere, with refinement into 94 regions, and cortical layers). The high-dimensional nature of this unique dataset and the possible connection between anatomy and gene expression pose challenges to data analysis. We developed the Brain Gene Expression Analysis Toolbox (downloadable at: www.brainarchitecture.org). The key functionalities include: determination of marker genes for brain regions, statistical analysis of brain-wide co-expression patterns, and the computation of brain-wide correlation maps with cell-type specific microarray data. The auxiliary dataset consisting of cell-type-specific transcriptomes (chapter 4) will be made available in the second version of the toolbox
