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Topics/Article : An article of ViBrism DB was selcted as Nucleic Acids Research Breakthrough article

An article "ViBrism DB: an interactive search and viewer platform for 2D/3D anatomical images of gene expression and co-expression networks" was published on Oct. 29, 2018 at Nucleic Acids Research <https://doi.org/10.1093/nar/gky951>. This article describes the achievement of INCF Japan Node Platform, ViBrism (Chaired by Yuko Okamura-Oho, Jissen Woman University, RIKEN and NPO BReNT-). It was selected as NAR Breakthrough Article.

The Journal Article

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

Authors:M. Morita, K. Shimokawa, M. Nishimura, S. Nakamura, Y. Tsujimura, S. Takemoto, T. Tawara, H. Yokota, S. Wemler, D. Miyamoto, H. Ikeno, A. Sato, T. Furuichi, N. Kobayashi, Y. Okumura, Y. Yamaguchi, Y. Okamura-Oho

Journal:Nucleic Acids Research, gky951 (2018)

Published Date:October 29, 2018

DOI: https://doi.org/10.1093/nar/gky951

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.

 

 on 2018-11-09 17:49:41 (202 reads)

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