A digital framework to build, visualize and analyze a gene expression atlas with cellular resolution in zebrafish early embryogenesis

Castro González, Carlos and Luengo Oroz, Miguel Ángel and Duloquin, Louise and Savy, Thierry and Rizzi, Barbara and Desnoulez, Sophie and Doursat, René and Kergosien, Yannick L. and Ledesma Carbayo, María Jesús and Bourgine, Paul and Peyriéras, Nadine and Santos Lleo, Andrés (2014). A digital framework to build, visualize and analyze a gene expression atlas with cellular resolution in zebrafish early embryogenesis. "Plos Computational Biology", v. 10 (n. 6); pp. 1-13. ISSN 1553-7358. https://doi.org/10.1371/journal.pcbi.1003670.

Description

Title: A digital framework to build, visualize and analyze a gene expression atlas with cellular resolution in zebrafish early embryogenesis
Author/s:
  • Castro González, Carlos
  • Luengo Oroz, Miguel Ángel
  • Duloquin, Louise
  • Savy, Thierry
  • Rizzi, Barbara
  • Desnoulez, Sophie
  • Doursat, René
  • Kergosien, Yannick L.
  • Ledesma Carbayo, María Jesús
  • Bourgine, Paul
  • Peyriéras, Nadine
  • Santos Lleo, Andrés
Item Type: Article
Título de Revista/Publicación: Plos Computational Biology
Date: June 2014
ISSN: 1553-7358
Volume: 10
Subjects:
Faculty: E.T.S.I. Telecomunicación (UPM)
Department: Ingeniería Electrónica
Creative Commons Licenses: Recognition - No derivative works - Non commercial

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Abstract

A gene expression atlas is an essential resource to quantify and understand the multiscale processes of embryogenesis in time and space. The automated reconstruction of a prototypic 4D atlas for vertebrate early embryos, using multicolor fluorescence in situ hybridization with nuclear counterstain, requires dedicated computational strategies. To this goal, we designed an original methodological framework implemented in a software tool called Match-IT. With only minimal human supervision, our system is able to gather gene expression patterns observed in different analyzed embryos with phenotypic variability and map them onto a series of common 3D templates over time, creating a 4D atlas. This framework was used to construct an atlas composed of 6 gene expression templates from a cohort of zebrafish early embryos spanning 6 developmental stages from 4 to 6.3 hpf (hours post fertilization). They included 53 specimens, 181,415 detected cell nuclei and the segmentation of 98 gene expression patterns observed in 3D for 9 different genes. In addition, an interactive visualization software, Atlas-IT, was developed to inspect, supervise and analyze the atlas. Match-IT and Atlas-IT, including user manuals, representative datasets and video tutorials, are publicly and freely available online. We also propose computational methods and tools for the quantitative assessment of the gene expression templates at the cellular scale, with the identification, visualization and analysis of coexpression patterns, synexpression groups and their dynamics through developmental stages.

More information

Item ID: 35892
DC Identifier: http://oa.upm.es/35892/
OAI Identifier: oai:oa.upm.es:35892
DOI: 10.1371/journal.pcbi.1003670
Official URL: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003670
Deposited by: Memoria Investigacion
Deposited on: 28 Jun 2015 09:55
Last Modified: 28 Jun 2015 09:55
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