Cell type-specific genes show striking and distinct patterns of spatial expression in the mouse brain

Younhee Ko, Seth A. Ament, James A. Eddy, Juan Caballero, John C. Earls, Leroy Hood, Nathan D. Price

Research output: Contribution to journalArticlepeer-review


To characterize gene expression patterns in the regional subdivisions of the mammalian brain, we integrated spatial gene expression patterns from the Allen Brain Atlas for the adult mouse with panels of cell type-specific genes for neurons, astrocytes, and oligodendrocytes frompreviously published transcriptome profiling experiments. We found that the combined spatial expression patterns of 170 neuron-specific transcripts revealed strikingly clear and symmetrical signatures for most of the brain's major subdivisions. Moreover, the brain expression spatial signatures correspond to anatomical structures and may even reflect developmental ontogeny. Spatial expression profiles of astrocyte-and oligodendrocyte-specific genes also revealed regional differences; these defined fewer regions and were less distinct but still symmetrical in the coronal plane. Follow-up analysis suggested that region-based clustering of neuron-specific genes was related to (i) a combination of individual genes with restricted expression patterns, (ii) region-specific differences in the relative expression of functional groups of genes, and (iii) regional differences in neuronal density. Products from some of these neuron-specific genes are present in peripheral blood, raising the possibility that they could reflect the activities of disease-or injury-perturbed networks and collectively function as biomarkers for clinical disease diagnostics.

Original languageEnglish (US)
Pages (from-to)3095-3100
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number8
StatePublished - Feb 19 2013
Externally publishedYes

ASJC Scopus subject areas

  • General

Fingerprint Dive into the research topics of 'Cell type-specific genes show striking and distinct patterns of spatial expression in the mouse brain'. Together they form a unique fingerprint.

Cite this