Novel genes located in the co-expression networks detected with Transcriptome Tomography
-
1
Brain Research Network (BReNt), Japan
-
2
RIKEN, Japan
-
3
Tohoku Medical Megabank Organization, Tohoku University, Japan
-
4
Tokyo University of Science, Japan
Detection of gene expression-anatomy association is crucial for understanding functions, in particular, of novel coding and non-coding genes. We have invented a framework for comprehensive gene expression density mapping on the whole three dimensional (3D) anatomical context, Transcriptome Tomography (ref.1): here, the methodology is shown in Movie 1. Measured expression densities are usable directly for gene-by-gene correlation analysis of co-expression, and then we have developed a novel bioinformatics framework for comprehensively assessing co-expression patterns that are latent within expression maps (paper in revision). Co-expression search using almost all genes expressed in the adult mouse brain can be done on our website: ViBrism-DB (Figure 1). In this presentation we would focus on previously uncharacterized mouse-specific genes that were co-expressed with genes encoding transcription factors and related molecules. The combinatorial expression of these genes associated with a discrete cell lineage of developmental stages seems to occur in the adult brain and the previously uncharacterized non-coding genes were located in a co-expression network position linking the combinations. This linkage suggests characteristics of these genes that coordinate multiple gene groups and create mouse-specific designs of neurogenesis.
Acknowledgements
This research was supported by funding from the RIKEN Strategic Programs for R&D (President’s Discretionary Fund) to H.Y., Y.O., K.S., et, al., JSPS KAKENHI Grant Number 25560428 to Y.O. and H.Y., JST Acceleration Utilization of University IP Program to Y.O., RIKEN Neuroinformatics Japan Center to T. F., and JSPS KAKENHI Grant Number 23300137 and 258057 to T. F..
References
1. Okamura-Oho, Y. et al. Transcriptome Tomography for Brain Analysis in the Web-Accessible Anatomical Space. PLoS One 7, e45373 (2012).
Keywords:
Gene Expression Profiling,
Brain Mapping,
digital atlasing,
co-expression networks,
Databases, Genetic
Conference:
Neuroinformatics 2014, Leiden, Netherlands, 25 Aug - 27 Aug, 2014.
Presentation Type:
Poster, not to be considered for oral presentation
Topic:
Genomics and genetics
Citation:
Okamura-Oho
Y,
Shimokawa
K,
Nishimura
M,
Takemoto
S,
Sato
A,
Furuichi
T and
Yokota
H
(2014). Novel genes located in the co-expression networks detected with Transcriptome Tomography.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2014.
doi: 10.3389/conf.fninf.2014.18.00022
Copyright:
The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers.
They are made available through the Frontiers publishing platform as a service to conference organizers and presenters.
The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated.
Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed.
For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions.
Received:
04 Apr 2014;
Published Online:
04 Jun 2014.
*
Correspondence:
Dr. Yuko Okamura-Oho, Brain Research Network (BReNt), Zushi-shi, Japan, yoho-tky@umin.ac.jp