Quantitative Biology

, Volume 1, Issue 1, pp 91–100

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

  • Pascal Grange
  • Michael Hawrylycz
  • Partha P. Mitra

DOI: 10.1007/s40484-013-0011-5

Cite this article as:
Grange, P., Hawrylycz, M. & Mitra, P.P. Quant Biol (2013) 1: 91. doi:10.1007/s40484-013-0011-5


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.

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Supplementary material

40484_2013_11_MOESM1_ESM.pdf (192 kb)
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Copyright information

© Higher Education Press and Springer-Verlag GmbH 2013

Authors and Affiliations

  • Pascal Grange
    • 1
  • 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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