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

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 BrainGeneExpressionAnalysis (BGEA), a Matlab toolbox available for download.

Graphical abstract

References

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ACKNOWLEDGMENTS

We thank Sharmila Banerjee-Basu, Idan Menashe, Eric C. Larsen, Hemant Bokil and Jason W. Bohland for discussions and collaboration. This research is supported by the NIH-NIDA Grant (1R21DA027644-01, Computational analysis of co-expression networks in the mouse and human brain).

RIGHTS & PERMISSIONS

2014 Higher Education Press and Springer-Verlag Berlin Heidelberg