Ex-vivo transcriptomic analysis on the web: a new platform of ViBrism DB for gene expression mapping and analysis

Event Abstract Back to Event Ex-vivo transcriptomic analysis on the web: a new platform of ViBrism DB for gene expression mapping and analysis Yuko Okamura-Oho1, 2*, Masahiko Morita2, Kazuro Shimokawa3, Masaomi Nishimura2, Takehiro Tawara2 and Hideo Yokota2 1 Brain Research Network (BReNt), Japan 2 RIKEN, Japan 3 Tohoku University, Japan Microtomy techniques for tomographic acquisition of thin-sliced material sections and their block-face images, followed by high-throughput measurements of gene expression densities in the materials, enable ex-vivo transcriptomic analysis of intricate spatial expression patterns of wide varieties of RNA molecules in the whole anatomical context of any materials of interest, such as the brain and the embryos(ref 1). Using our microtomy technique, transcriptome tomography, we have created a database, ViBrism DB, in which measured expression densities are used for three dimensional (3D) expression map reconstruction and the maps can be superimposed on other voxel based images of the material (ref 2). Also the densities are directly used for co-expression analysis (ref 3). Here, we have launched a new platform of the DB for ex-vivo transcriptomic analysis of mouse developing brains on the web. The platform is equipped with a WEB-GL based 3D viewer of expression maps overlaid on the MRI images and anatomical region maps. Also co-expression network graphs of genes of interest are created and can be viewed with the expression maps. We will demonstrate integrated analysis of anatomical maps and topological co-expression graphs in the developing brains on this web-based platform. All users of the microtomy technique can use this platform to upload their own data sets on the DB and view their maps and networks on the website. Acknowledgements A part of this work was conducted within the Waxholm Space Task Force of the International Neuroinformatics Coordinating Facility (INCF) Program on Digital Brain Atlasing. References 1. Crosetto, N. et al. Spatially resolved transcriptomics and beyond. Nat. Rev. Genet. 16, 57–66 (2014). 2. Okamura-Oho, Y. et al. Transcriptome tomography for brain analysis in the web-accessible anatomical space. PLoS One 7, e45373 (2012). 3. 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: Microtomy, Transcriptomic Analysis, 3D Reconstruction, gene expression map, co-expression network Conference: Neuroinformatics 2015, Cairns, Australia, 20 Aug - 22 Aug, 2015. Presentation Type: Demo, not to be considered for oral presentation Topic: Digital atlasing Citation: Okamura-Oho Y, Morita M, Shimokawa K, Nishimura M, Tawara T and Yokota H (2015). Ex-vivo transcriptomic analysis on the web: a new platform of ViBrism DB for gene expression mapping and analysis. Front. Neurosci. Conference Abstract: Neuroinformatics 2015. doi: 10.3389/conf.fnins.2015.91.00043 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: 20 Apr 2015; Published Online: 05 Aug 2015. * Correspondence: Dr. Yuko Okamura-Oho, Brain Research Network (BReNt), Zushi-shi, Japan, yoho-tky@umin.ac.jp Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Yuko Okamura-Oho Masahiko Morita Kazuro Shimokawa Masaomi Nishimura Takehiro Tawara Hideo Yokota Google Yuko Okamura-Oho Masahiko Morita Kazuro Shimokawa Masaomi Nishimura Takehiro Tawara Hideo Yokota Google Scholar Yuko Okamura-Oho Masahiko Morita Kazuro Shimokawa Masaomi Nishimura Takehiro Tawara Hideo Yokota PubMed Yuko Okamura-Oho Masahiko Morita Kazuro Shimokawa Masaomi Nishimura Takehiro Tawara Hideo Yokota Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.