, Volume 7, Issue 2, pp 67–80 | Cite as

Gene expression analyses reveal molecular relationships among 20 regions of the human CNS

  • Richard B. RothEmail author
  • Peter Hevezi
  • Jerry Lee
  • Dorian Willhite
  • Sandra M. Lechner
  • Alan C. Foster
  • Albert Zlotnik
Original Article


Transcriptional profiling was performed to survey the global expression patterns of 20 anatomically distinct sites of the human central nervous system (CNS). Forty-five non-CNS tissues were also profiled to allow for comparative analyses. Using principal component analysis and hierarchical clustering, we were able to show that the expression patterns of the 20 CNS sites profiled were significantly different from all non-CNS tissues and were also similar to one another, indicating an underlying common expression signature. By focusing our analyses on the 20 sites of the CNS, we were able to show that these 20 sites could be segregated into discrete groups with underlying similarities in anatomical structure and, in many cases, functional activity. These findings suggest that gene expression data can help define CNS function at the molecular level. We have identified subsets of genes with the following patterns of expression: (1) across the CNS, suggesting homeostatic/housekeeping function; (2) in subsets of functionally related sites of the CNS identified by our unsupervised learning analyses; and (3) in single sites within the CNS, indicating their participation in distinct site-specific functions. By performing network analyses on these gene sets, we identified many pathways that are upregulated in particular sites of the CNS, some of which were previously described in the literature, validating both our dataset and approach. In summary, we have generated a database of gene expression that can be used to gain valuable insight into the molecular characterization of functions carried out by different sites of the human CNS.


Central nervous system Human Transcriptional profiling Microarray Network analysis 



Adenosine A2a receptor


Amphiphysin (Stiff–Man syndrome with breast cancer 128 kDa autoantigen)


Calcium channel, voltage-dependent, P/Q type, alpha 1A subunit


Calcium channel, voltage-dependent, L type, alpha 1B subunit


Central nervous system


Class I MHC-restricted T cell-associated molecule


Cytosine triphosphate


Discs, large homologue 2, chapsyn-110 (Drosophila)


Discs, large homologue 4 (Drosophila)


Discs, large (Drosophila) homologue-associated protein 1


Dynamin 1


Dopamine receptor D2EDNRB-endothelin receptor type B


Epidermal growth factor receptor pathway substrate 15


FBJ murine osteosarcoma viral oncogene homologue B


FYN oncogene related to SRC, FGR, and YES


Gamma-aminobutyric acid (GABA) A receptor, alpha 6


G-protein coupled receptor


Glutamate receptor, ionotropic, kainate 2


Glutamate receptor, ionotropic, N-methyl D-aspartate 1


Glutamate receptor, metabotropic 3


Ingenuity Pathways Knowledge Base


In vitro transcription


Myelin basic protein


Principal component analysis


Polymerase chain reaction


Pro-melanin-concentrating hormone


Postmortem interval


Peripheral nervous system


Protein tyrosine phosphatase, nonreceptor type 5


Quantitative polymerase chain reaction


RAB3A, member RAS oncogene family


Robust multiarray analysis; robust multichip average


Ribonucleic acid


Secreted frizzled-related protein 4


Solute carrier family 1 (glial high affinity glutamate transporter), member 3


Synaptosomal-associated protein, 25 kDa


Synaptotagmin I


Synaptotagmin III


Synaptotagmin IV


Tyrosine hydroxylase


Target of interest


Uridine triphosphate


Vesicle-associated membrane protein 2 (synaptobrevin 2)



We thank Dr. Richard A. Maki for helpful discussion and critical reading of the manuscript.

Supplementary material

10048_2006_32_MOESM1_ESM.pdf (57 kb)
Table S1 (PDF 58 kb)
10048_2006_32_MOESM2_ESM.pdf (63 kb)
Table S2 (PDF 65 kb)
10048_2006_32_MOESM3_ESM.pdf (68 kb)
Table S3 (PDF 70 kb)


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Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Richard B. Roth
    • 1
    Email author
  • Peter Hevezi
    • 1
  • Jerry Lee
    • 1
  • Dorian Willhite
    • 1
  • Sandra M. Lechner
    • 2
  • Alan C. Foster
    • 2
  • Albert Zlotnik
    • 1
  1. 1.Department of Molecular Medicine, Neurocrine Biosciences, IncorporatedSan DiegoUSA
  2. 2.Department of Neuroscience, Neurocrine Biosciences, IncorporatedSan DiegoUSA

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