Skip to main content
SpringerLink
Log in

The Allen Brain Atlas

  • Chapter
Springer Handbook of Bio-/Neuroinformatics

Part of the book series: Springer Handbooks ((SHB))

Abstract

The Allen Brain Atlas is an online publicly available resource that integrates gene expression and connectivity data with neuroanatomical information for the mouse, human, and non-human primate. Launched in 2004 by the Allen Institute for Brain Science, the portal currently receives about 45000 unique users each month. More than one petabyte of in situ hybridization imagery and over 240 million microarray data points from six adult human brains representing 3700 tissue samples have been generated to date. As one of the most comprehensive gene expression resources for the nervous system, scientists regularly use these resources to study the expression profile of genes in the various regions of the brain. Additional usage includes searching for biomarkers, correlating gene expression to neuroanatomy, and other large-scale correlative data analysis. This chapter reviews the resources available and describes how they were constructed to enable development of visualization and search tools to analyze the massive amount of data generated. Finally, examples are provided on how these tools can be leveraged for scientific discovery.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 269.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 349.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Abbreviations

2-D:

two-dimensional

3-D:

three-dimensional

AGEA:

Anatomic Gene Expression Atlas

API:

application programming interface

CC:

cellular component

CNS:

central nervous system

CSV:

comma-separated values

Cb:

cerebellum

CbN:

cerebellar nuclei

DG:

dentate gyrus

DTI:

diffusion tensor imaging

EIV:

Experiment Image Viewer

FGF:

fibroblast growth factor

GC:

Granger causality

GO:

gene ontology

GP:

globus pallidus

Hip:

hippocampus

ISH:

in situ hybridization

JSON:

JavaScript object notation

MAPK:

mitogen-activated protein kinase

MET:

met proto-oncogene

MNI:

4-methoxy-7-nitroindolinyl

MR:

magnetic resonance

MRI:

magnetic resonance imaging

NIH:

National Institutes of Health

Pu:

putamen

REST:

representational state transfer

RN:

red nucleus

RNA:

ribonucleic acid

SCG:

subcallosal gyrus

SPM:

Statistical Parametric Mapping

URL:

unified resource locator

VTA:

ventral tegmental area

WGCNA:

weighted gene co-expression network analysis

XML:

extensible markup language

References

  1. Allen Brain Institute: Brain Atlas, available online at www.brain-map.org

  2. E.S. Lein, M.J. Hawrylycz, N. Ao, M. Ayres, A. Bensinger, A. Bernard, A.F. Boe, M.S. Boguski, K.S. Brockway, E.J. Byrnes, et al.: Genome-wide atlas of gene expression in the adult mouse brain, Nature 445, 168–176 (2007)

    Article  Google Scholar 

  3. L.L. Ng, S.D. Pathak, C.L. Kuan, C. Lau, H. Dong, A.J. Sodt, C.N. Dang, B. Avants, P. Yushkevich, J.C. Gee, et al.: Neuroinformatics for genome-wide 3-D gene expression mapping in the mouse brain, IEEE Trans. Comput. Biol. Bioinforma. 4, 382–393 (2007)

    Article  Google Scholar 

  4. L.L. Ng, S.M. Sunkin, D. Feng, C. Lau, C. Dang, M.J. Hawrylycz: Large-scale neuroinformatics for in situ hybridization data in the mouse brain, Int. Rev. Neurobiol. 104, 159–182 (2012)

    Article  Google Scholar 

  5. L. Madisen, T.A. Zwingman, S.M. Sunkin, S.W. Oh, H.A. Zariwala, H. Gu, L.L. Ng, R.D. Palmiter, M.J. Hawrylycz, A.R. Jones, et al.: A robust and high-throughput cre reporting and characterization system for the whole mouse brain, Nat. Neurosci. 13, 133–140 (2010)

    Article  Google Scholar 

  6. L. Madisen, T. Mao, H. Koch, J.M. Zhuo, A. Berenyi, S. Fujisawa, Y.W. Hsu, A.J. Garcia III, X. Gu, S. Zanella, et al.: A toolbox of cre-dependent optogenetic transgenic mice for light-induced activation and silencing, Nat. Neurosci. 15, 793–802 (2012)

    Article  Google Scholar 

  7. H. Zeng, L. Madisen: Mouse transgenic approaches in optogenetics, Prog. Brain Res. 196, 193–213 (2012)

    Article  Google Scholar 

  8. H.W. Dong: The Allen Reference Atlas: A Digital Color Brain Atlas of the C57BL/6J Male Mouse (Wiley, Hoboken 2008)

    Google Scholar 

  9. P. Xu, J. Xu, Z. Li, Z. Yang: Expression of TRPC6 in renal cortex and hippocampus of mouse during postnatal development, PLoS ONE 7, e38503 (2012)

    Article  Google Scholar 

  10. J. Zhou, W. Du, K. Zhou, Y. Tai, H. Yao, Y. Jia, Y. Ding, Y. Wang: Critical role of TRPC6 channels in the formation of excitatory synapses, Nat. Neurosci. 11, 741–743 (2008)

    Article  Google Scholar 

  11. Y. Tai, S. Feng, R. Ge, W. Du, X. Zhang, Z. He, Y. Wang: TRPC6 channels promote dendritic growth via the CaMKIV-CREB pathway, J. Cell Sci. 121, 2301–2307 (2008)

    Article  Google Scholar 

  12. K. Leuner, W. Li, M.D. Amaral, S. Rudolph, G. Calfa, A.M. Schuwald, C. Harteneck, T. Inoue, L. Pozzo-Miller: Hyperforin modulates dendritic spine morphology in hippocampal pyramidal neurons by activating Ca2+-permeable TRPC6 channels, Hippocampus 23, 40–52 (2013)

    Article  Google Scholar 

  13. M. Hawrylycz, L. Ng, D. Page, J. Morris, C. Lau, S. Faber, V. Faber, S. Sunkin, V. Menon, E. Lein, et al.: Multi-scale correlation structure of gene expression in the brain, Neural Netw. 24, 933–942 (2011)

    Article  Google Scholar 

  14. H. Hagihara, K. Toyama, N. Yamasaki, T. Miyakawa: Dissection of hippocampal dentate gyrus from adult mouse, J. Vis. Exp. 17(33), 1543 (2009)

    Google Scholar 

  15. J. Hauser, T.A. Sontag, O. Tucha, K.W. Lange: The effects of the neurotoxin DSP4 on spatial learning and memory in Wistar rats, Atten. Defic. Hyperact. Disord. 4, 93–99 (2012)

    Article  Google Scholar 

  16. A. Lavado, O.V. Lagutin, L.M. Chow, S.J. Baker, G. Oliver: Prox1 is required for granule cell maturation and intermediate progenitor maintenance during brain neurogenesis, PLoS Biol. 8, e1000460 (2010)

    Article  Google Scholar 

  17. M.J. Hawrylycz, E.S. Lein, A.L. Guillozet-Bongaarts, E.H. Shen, L. Ng, J.A. Miller, L.N. van de Lagemaat, K.A. Smith, A. Ebbert, Z.L. Riley, et al.: An anatomically comprehensive atlas of the adult human brain transcriptome, Nature 489, 391–399 (2012)

    Article  Google Scholar 

  18. A.M. Dale, B. Fischl, M.I. Sereno: Cortical surface-based analysis. I. Segmentation and surface reconstruction, NeuroImage 9, 179–194 (1999)

    Article  Google Scholar 

  19. www.genomics.agilent.com

  20. www.bioimagesuite.org

  21. R. Seger, E.G. Krebs: The MAPK signaling cascade, FASEB J. 9, 726–735 (1995)

    Google Scholar 

  22. B. Reuss, O. von Bohlen und Halbach: Fibroblast growth factors and their receptors in the central nervous system, Cell Tissue Res. 313, 139–157 (2003)

    Article  Google Scholar 

  23. S. Zechel, S. Werner, K. Unsicker, O. von Bohlen und Halbach: Expression and functions of fibroblast growth factor 2 (FGF-2) in hippocampal formation, Neuroscientist 16, 357–373 (2010)

    Article  Google Scholar 

  24. http://david.abcc.ncifcrf.gov/

  25. C.M. Deber, S.J. Reynolds: Central nervous system myelin: Structure, function, and pathology, Clin. Biochem. 24, 113–134 (1991)

    Article  Google Scholar 

  26. S.M. Sunkin, L. Ng, C. Lau, T. Dolbeare, T.L. Gilbert, C.L. Thompson, M. Hawrylycz, C. Dang: Allen Brain Atlas: An integrated spatio-temporal portal for exploring the central nervous system, Nucleic Acids Res. 41(41), D996–D1008 (2012)

    Google Scholar 

  27. http://en.wikipedia.org/wiki/Representational_state_transfer

  28. P. Langfelder, S. Horvath: WGCNA: An R package for weighted correlation network analysis, BMC Bioinformat. 9, 559 (2008)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Modeling, Analysis, and Theory, Allen Institute for Brain Science, 551 N. 34th St., 98103, Seattle, WA, USA

    Michael Hawrylycz

  2. Department of Technology, Allen Institute for Brain Science, 551 N. 34th Street, 98103, Seattle, WA, USA

    Lydia Ng

  3. Department of Technology, Allen Institute for Brain Science, 34th St., 98103, Seattle, WA, USA

    David Feng

  4. Scientific Program Management, Allen Institute for Brain Science, 551 N. 34th Street, 98103, Seattle, WA, USA

    Susan Sunkin

  5. Department of Technology, Allen Institute for Brain Science, 551 N. 34th Street, 98103, Seattle, WA, USA

    Aaron Szafer

  6. Department of Technology, Allen Institute for Brain Science, 34th St., 98103, Seattle, WA, USA

    Chinh Dang

Authors
  1. Michael Hawrylycz
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lydia Ng
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. David Feng
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Susan Sunkin
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Aaron Szafer
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Chinh Dang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Michael Hawrylycz , Lydia Ng , David Feng , Susan Sunkin , Aaron Szafer or Chinh Dang .

Editor information

Editors and Affiliations

  1. KEDRI – Knowledge Engineering and Discovery Research Institute, Auckland University of Technology, 120 Mayoral Drive, 1010, Auckland, New Zealand

    Nikola Kasabov

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer-Verlag

About this chapter

Cite this chapter

Hawrylycz, M., Ng, L., Feng, D., Sunkin, S., Szafer, A., Dang, C. (2014). The Allen Brain Atlas. In: Kasabov, N. (eds) Springer Handbook of Bio-/Neuroinformatics. Springer Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30574-0_62

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-30574-0_62

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-30573-3

  • Online ISBN: 978-3-642-30574-0

  • eBook Packages: EngineeringEngineering (R0)

Publish with us

Policies and ethics

Search

Navigation