TY - JOUR
T1 - ViBrism DB
T2 - An interactive search and viewer platform for 2D/3D anatomical images of gene expression and co-expression networks
AU - Morita, Masahiko
AU - Shimokawa, Kazuro
AU - Nishimura, Masaomi
AU - Nakamura, Sakiko
AU - Tsujimura, Yuki
AU - Takemoto, Satoko
AU - Tawara, Takehiro
AU - Yokota, Hideo
AU - Wemler, Shuhei
AU - Miyamoto, Daisuke
AU - Ikeno, Hidetoshi
AU - Sato, Akira
AU - Furuichi, Teiichi
AU - Kobayashi, Norio
AU - Okumura, Yoshihiro
AU - Yamaguchi, Yoko
AU - Okamura-Oho, Yuko
N1 - Publisher Copyright:
© The Author(s) 2018.
Copyright:
Copyright 2019 Elsevier B.V., All rights reserved.
PY - 2019/1/8
Y1 - 2019/1/8
N2 - 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 regionspecific 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 ofmicrotomy-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 scenesetting parameters. The DB has multiple links and is expandable by community activity.
AB - 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 regionspecific 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 ofmicrotomy-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 scenesetting parameters. The DB has multiple links and is expandable by community activity.
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U2 - 10.1093/nar/gky951
DO - 10.1093/nar/gky951
M3 - Article
C2 - 30371824
AN - SCOPUS:85059796374
VL - 47
SP - D859-D866
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - D1
ER -