Computational neuroanatomy and co-expression of genes in the adult mouse brain, analysis tools for the Allen Brain Atlas

TL;DR

This paper reviews and introduces new computational methods for analyzing large-scale gene expression data in the mouse brain, utilizing the Allen Brain Atlas and a Matlab toolbox to explore co-expression networks and their geometry.

Contribution

It presents novel high-dimensional geometric methods and simulations for analyzing brain-wide gene expression data, implemented in an accessible Matlab toolbox.

Findings

New methods reveal geometric structure of gene expression data

Application to NicSNP genes uncovers co-expression patterns

Tools facilitate large-scale spatial gene expression analysis

Abstract

We review quantitative methods and software developed to analyze genome-scale, brain-wide spatially-mapped gene-expression data. We expose new methods based on the underlying high-dimensional geometry of voxel space and gene space, and on simulations of the distribution of co-expression networks of a given size. We apply them to the Allen Atlas of the adult mouse brain, and to the co-expression network of a set of genes related to nicotine addiction retrieved from the NicSNP database. The computational methods are implemented in {\ttfamily{BrainGeneExpressionAnalysis}}, a Matlab toolbox available for download.