Anatomical and topological expression analysis of the mouse transcriptome in the virtual 3D MRI image spaces of the postnatal brain stages
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1
RIKEN, Japan
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2
Brain Research Network (BReNt), Japan
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3
Jissen Women's University, Japan
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4
Tohoku University, Japan
Using a microtomy-based gene expression measurement technique, Transcriptome Tomography1, we mapped spatial expression-density patterns of comprehensive transcripts on the 3D MRI images of the mouse brains at three maturation stages after the birth (http://vibrism.neuroinf.jp/): 52.3 % were known gene products and the rest were un-characterized transcripts of coding and non-coding genes including putative long-intergenic non-coding RNAs. To examine expression patterns of a large number of transcripts, we have proposed an integrated analysis platform of expression maps and the co-expression networks, in which the maps are located in the node position of the network depicted with a force-based stochastic method2. In the maturation stages as well as the adult stage that we reported previously, distributions of the network edge numbers followed the power law and the networks were rich in functionally related genes. The networks represented anatomical areas of the function without adding any anatomical information. Here we show the analysis of consistent co-expression through the stages and the analysis of diverse expression changing along the maturation covering the whole brain anatomical context.
Acknowledgements
This work was supported by INCF Japan node (J-node) members in RIKEN Neuroinformatics Japan Center (NIJC).
Funding: JSPS KAKENHI Grant Number 25560428, 26280110, 268032 and 15HP8038, and JST Acceleration Utilization of University IP Program to Y.O., and the NIJC funding support to the ViBrism DB Platform Committee.
References
1. Okamura-Oho, Y. et al. Transcriptome tomography for brain analysis in the web-accessible anatomical space. PLoS One 7, e45373 (2012).
2. Okamura-Oho, Y. et al. Broad integration of expression maps and co-expression networks compassing novel gene functions in the brain. Sci. Rep. 4, 6969 (2014).
Keywords:
gene expression map,
Microtomy,
3D Reconstruction,
Transcriptomic Analysis,
co-expression network
Conference:
Neuroinformatics 2016, Reading, United Kingdom, 3 Sep - 4 Sep, 2016.
Presentation Type:
Poster
Topic:
Genomics and genetics
Citation:
Okamura-Oho
Y,
Shimokawa
K,
Morita
M,
Nishimura
M and
Yokota
H
(2016). Anatomical and topological expression analysis of the mouse transcriptome in the virtual 3D MRI image spaces of the postnatal brain stages.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2016.
doi: 10.3389/conf.fninf.2016.20.00072
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Received:
25 May 2016;
Published Online:
18 Jul 2016.
*
Correspondence:
Dr. Yuko Okamura-Oho, RIKEN, Wako-Shi, Japan, yoho-tky@umin.ac.jp