Quantitative expression profile of distinct functional regions in the adult mouse brain

Takeya Kasukawa, Koh hei Masumoto, Itoshi Nikaido, Mamoru Nagano, Kenichiro D. Uno, Kaori Tsujino, Carina Hanashima, Yasufumi Shigeyoshi, Hiroki R. Ueda

Research output: Contribution to journalArticle

44 Citations (Scopus)

Abstract

The adult mammalian brain is composed of distinct regions with specialized roles including regulation of circadian clocks, feeding, sleep/awake, and seasonal rhythms. To find quantitative differences of expression among such various brain regions, we conducted the BrainStars (B*) project, in which we profiled the genome-wide expression of ~50 small brain regions, including sensory centers, and centers for motion, time, memory, fear, and feeding. To avoid confounds from temporal differences in gene expression, we sampled each region every 4 hours for 24 hours, and pooled the samples for DNA-microarray assays. Therefore, we focused on spatial differences in gene expression. We used informatics to identify candidate genes with expression changes showing high or low expression in specific regions. We also identified candidate genes with stable expression across brain regions that can be used as new internal control genes, and ligand-receptor interactions of neurohormones and neurotransmitters. Through these analyses, we found 8,159 multi-state genes, 2,212 regional marker gene candidates for 44 small brain regions, 915 internal control gene candidates, and 23,864 inferred ligand-receptor interactions. We also found that these sets include well-known genes as well as novel candidate genes that might be related to specific functions in brain regions. We used our findings to develop an integrated database (http://brainstars.org/) for exploring genome-wide expression in the adult mouse brain, and have made this database openly accessible. These new resources will help accelerate the functional analysis of the mammalian brain and the elucidation of its regulatory network systems.

Original languageEnglish
Article numbere23228
JournalPLoS One
Volume6
Issue number8
DOIs
Publication statusPublished - 2011
Externally publishedYes

Fingerprint

Brain
Genes
brain
mice
genes
Gene Expression
Neurotransmitter Agents
Gene expression
Genome
Databases
Ligands
neurohormones
gene expression
receptors
Circadian Clocks
Informatics
genome
neurotransmitters
Oligonucleotide Array Sequence Analysis
sleep

ASJC Scopus subject areas

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Kasukawa, T., Masumoto, K. H., Nikaido, I., Nagano, M., Uno, K. D., Tsujino, K., ... Ueda, H. R. (2011). Quantitative expression profile of distinct functional regions in the adult mouse brain. PLoS One, 6(8), [e23228]. https://doi.org/10.1371/journal.pone.0023228

Quantitative expression profile of distinct functional regions in the adult mouse brain. / Kasukawa, Takeya; Masumoto, Koh hei; Nikaido, Itoshi; Nagano, Mamoru; Uno, Kenichiro D.; Tsujino, Kaori; Hanashima, Carina; Shigeyoshi, Yasufumi; Ueda, Hiroki R.

In: PLoS One, Vol. 6, No. 8, e23228, 2011.

Research output: Contribution to journalArticle

Kasukawa, T, Masumoto, KH, Nikaido, I, Nagano, M, Uno, KD, Tsujino, K, Hanashima, C, Shigeyoshi, Y & Ueda, HR 2011, 'Quantitative expression profile of distinct functional regions in the adult mouse brain', PLoS One, vol. 6, no. 8, e23228. https://doi.org/10.1371/journal.pone.0023228
Kasukawa T, Masumoto KH, Nikaido I, Nagano M, Uno KD, Tsujino K et al. Quantitative expression profile of distinct functional regions in the adult mouse brain. PLoS One. 2011;6(8). e23228. https://doi.org/10.1371/journal.pone.0023228
Kasukawa, Takeya ; Masumoto, Koh hei ; Nikaido, Itoshi ; Nagano, Mamoru ; Uno, Kenichiro D. ; Tsujino, Kaori ; Hanashima, Carina ; Shigeyoshi, Yasufumi ; Ueda, Hiroki R. / Quantitative expression profile of distinct functional regions in the adult mouse brain. In: PLoS One. 2011 ; Vol. 6, No. 8.
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