A digital framework to build, visualize and analyze a gene expression atlas with cellular resolution in zebrafish early embryogenesis.
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,...
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Public Library of Science (PLoS)
2014
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oai:doaj.org-article:9619d83b198644029b3ea2cb36ca42382021-11-11T05:52:06ZA digital framework to build, visualize and analyze a gene expression atlas with cellular resolution in zebrafish early embryogenesis.1553-734X1553-735810.1371/journal.pcbi.1003670https://doaj.org/article/9619d83b198644029b3ea2cb36ca42382014-06-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24945246/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358A 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.Carlos Castro-GonzálezMiguel A Luengo-OrozLouise DuloquinThierry SavyBarbara RizziSophie DesnoulezRené DoursatYannick L KergosienMaría J Ledesma-CarbayoPaul BourgineNadine PeyriérasAndrés SantosPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 10, Iss 6, p e1003670 (2014) |
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DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Biology (General) QH301-705.5 |
| spellingShingle |
Biology (General) QH301-705.5 Carlos Castro-González Miguel A Luengo-Oroz Louise Duloquin Thierry Savy Barbara Rizzi Sophie Desnoulez René Doursat Yannick L Kergosien María J Ledesma-Carbayo Paul Bourgine Nadine Peyriéras Andrés Santos A digital framework to build, visualize and analyze a gene expression atlas with cellular resolution in zebrafish early embryogenesis. |
| description |
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. |
| format |
article |
| author |
Carlos Castro-González Miguel A Luengo-Oroz Louise Duloquin Thierry Savy Barbara Rizzi Sophie Desnoulez René Doursat Yannick L Kergosien María J Ledesma-Carbayo Paul Bourgine Nadine Peyriéras Andrés Santos |
| author_facet |
Carlos Castro-González Miguel A Luengo-Oroz Louise Duloquin Thierry Savy Barbara Rizzi Sophie Desnoulez René Doursat Yannick L Kergosien María J Ledesma-Carbayo Paul Bourgine Nadine Peyriéras Andrés Santos |
| author_sort |
Carlos Castro-González |
| title |
A digital framework to build, visualize and analyze a gene expression atlas with cellular resolution in zebrafish early embryogenesis. |
| title_short |
A digital framework to build, visualize and analyze a gene expression atlas with cellular resolution in zebrafish early embryogenesis. |
| title_full |
A digital framework to build, visualize and analyze a gene expression atlas with cellular resolution in zebrafish early embryogenesis. |
| title_fullStr |
A digital framework to build, visualize and analyze a gene expression atlas with cellular resolution in zebrafish early embryogenesis. |
| title_full_unstemmed |
A digital framework to build, visualize and analyze a gene expression atlas with cellular resolution in zebrafish early embryogenesis. |
| title_sort |
digital framework to build, visualize and analyze a gene expression atlas with cellular resolution in zebrafish early embryogenesis. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2014 |
| url |
https://doaj.org/article/9619d83b198644029b3ea2cb36ca4238 |
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