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Nucleic Acids Res. 2019 Jan 8;47(D1):D859-D866. doi: 10.1093/nar/gky951.

ViBrism DB: an interactive search and viewer platform for 2D/3D anatomical images of gene expression and co-expression networks.

Author information

1
RIKEN Center for Advanced Photonics, Wako, Saitama 351-0198, Japan.
2
Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8575, Japan.
3
Wemler Software, Nerima, Tokyo 177-0042, Japan.
4
Graduate School of Engineering, The University of Tokyo, Meguro, Tokyo 153-0041, Japan.
5
School of Human Science and Environment, University of Hyogo, Himeji, Hyogo 670-0092, Japan.
6
Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan.
7
Head Office for Information Systems and Cybersecurity, RIKEN, Wako, Saitama 351-0198, Japan.
8
RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan.
9
Faculty of Human Life Science, Jissen Women's University, Hino, Tokyo 191-8510, Japan.

Abstract

Understanding anatomical structures and biological functions based on gene expression is critical in a systemic approach to address the complexity of the mammalian brain, where >25 000 genes are expressed in a precise manner. Co-expressed genes are thought to regulate cell type- or region-specific brain functions. Thus, well-designed data acquisition and visualization systems for profiling combinatorial gene expression in relation to anatomical structures are crucial. To this purpose, using our techniques of microtomy-based gene expression measurements and WebGL-based visualization programs, we mapped spatial expression densities of genome-wide transcripts to the 3D coordinates of mouse brains at four post-natal stages, and built a database, ViBrism DB (http://vibrism.neuroinf.jp/). With the DB platform, users can access a total of 172 022 expression maps of transcripts, including coding, non-coding and lncRNAs in the whole context of 3D magnetic resonance (MR) images. Co-expression of transcripts is represented in the image space and in topological network graphs. In situ hybridization images and anatomical area maps are browsable in the same space of 3D expression maps using a new browser-based 2D/3D viewer, BAH viewer. Created images are shareable using URLs, including scene-setting parameters. The DB has multiple links and is expandable by community activity.

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