Quantitative Biology

, Volume 1, Issue 1, pp 91–100 | Cite as

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

  • Pascal GrangeEmail author
  • Michael Hawrylycz
  • Partha P. Mitra


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 coexpression 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.


Expression Energy Adult Mouse Brain Allen Brain Voxel Space Allen Brain Atlas 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Supplementary material

40484_2013_11_MOESM1_ESM.pdf (192 kb)
Supplementary material, approximately 192 KB.


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Copyright information

© Higher Education Press and Springer-Verlag GmbH 2013

Authors and Affiliations

  • Pascal Grange
    • 1
    Email author
  • Michael Hawrylycz
    • 2
  • Partha P. Mitra
    • 1
  1. 1.Cold Spring Harbor LaboratoryCold Spring HarborNew YorkUSA
  2. 2.Allen Institute for Brain ScienceWashingtonUSA

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