Cell-type-specific microarray data and the Allen atlas: quantitative analysis of brain-wide patterns of correlation and density

Abstract

The Allen Atlas of the adult mouse brain is used to estimate the region-specificity of 64 cell types whose transcriptional profile in the mouse brain has been measured in microarray experiments. We systematically analyze the preliminary results presented in [arXiv:1111.6217], using the techniques implemented in the Brain Gene Expression Analysis toolbox. In particular, for each cell-type-specific sample in the study, we compute a brain-wide correlation profile to the Allen Atlas, and estimate a brain-wide density profile by solving a quadratic optimization problem at each voxel in the mouse brain. We characterize the neuroanatomical properties of the correlation and density profiles by ranking the regions of the left hemisphere delineated in the Allen Reference Atlas. We compare these rankings to prior biological knowledge of the brain region from which the cell-type-specific sample was extracted.