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The Tomato Expression Atlas

SUMMARY: With the development of new high-throughput DNA sequencing technologies and decreasing costs, large gene expression datasets are being generated at an accelerating rate, but can be complex to visualize. New, more interactive and intuitive tools are needed to visualize the spatiotemporal con...

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Autores principales: Fernandez-Pozo, Noe, Zheng, Yi, Snyder, Stephen I, Nicolas, Philippe, Shinozaki, Yoshihito, Fei, Zhangjun, Catala, Carmen, Giovannoni, James J, Rose, Jocelyn K.C, Mueller, Lukas A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860121/
https://www.ncbi.nlm.nih.gov/pubmed/28379331
http://dx.doi.org/10.1093/bioinformatics/btx190
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author Fernandez-Pozo, Noe
Zheng, Yi
Snyder, Stephen I
Nicolas, Philippe
Shinozaki, Yoshihito
Fei, Zhangjun
Catala, Carmen
Giovannoni, James J
Rose, Jocelyn K.C
Mueller, Lukas A
author_facet Fernandez-Pozo, Noe
Zheng, Yi
Snyder, Stephen I
Nicolas, Philippe
Shinozaki, Yoshihito
Fei, Zhangjun
Catala, Carmen
Giovannoni, James J
Rose, Jocelyn K.C
Mueller, Lukas A
author_sort Fernandez-Pozo, Noe
collection PubMed
description SUMMARY: With the development of new high-throughput DNA sequencing technologies and decreasing costs, large gene expression datasets are being generated at an accelerating rate, but can be complex to visualize. New, more interactive and intuitive tools are needed to visualize the spatiotemporal context of expression data and help elucidate gene function. Using tomato fruit as a model, we have developed the Tomato Expression Atlas to facilitate effective data analysis, allowing the simultaneous visualization of groups of genes at a cell/tissue level of resolution within an organ, enhancing hypothesis development and testing in addition to candidate gene identification. This atlas can be adapted to different types of expression data from diverse multicellular species. AVAILABILITY AND IMPLEMENTATION: The Tomato Expression Atlas is available at http://tea.solgenomics.net/. Source code is available at https://github.com/solgenomics/Tea. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-58601212018-03-23 The Tomato Expression Atlas Fernandez-Pozo, Noe Zheng, Yi Snyder, Stephen I Nicolas, Philippe Shinozaki, Yoshihito Fei, Zhangjun Catala, Carmen Giovannoni, James J Rose, Jocelyn K.C Mueller, Lukas A Bioinformatics Applications Notes SUMMARY: With the development of new high-throughput DNA sequencing technologies and decreasing costs, large gene expression datasets are being generated at an accelerating rate, but can be complex to visualize. New, more interactive and intuitive tools are needed to visualize the spatiotemporal context of expression data and help elucidate gene function. Using tomato fruit as a model, we have developed the Tomato Expression Atlas to facilitate effective data analysis, allowing the simultaneous visualization of groups of genes at a cell/tissue level of resolution within an organ, enhancing hypothesis development and testing in addition to candidate gene identification. This atlas can be adapted to different types of expression data from diverse multicellular species. AVAILABILITY AND IMPLEMENTATION: The Tomato Expression Atlas is available at http://tea.solgenomics.net/. Source code is available at https://github.com/solgenomics/Tea. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2017-08-01 2017-03-30 /pmc/articles/PMC5860121/ /pubmed/28379331 http://dx.doi.org/10.1093/bioinformatics/btx190 Text en © The Author 2017. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Fernandez-Pozo, Noe
Zheng, Yi
Snyder, Stephen I
Nicolas, Philippe
Shinozaki, Yoshihito
Fei, Zhangjun
Catala, Carmen
Giovannoni, James J
Rose, Jocelyn K.C
Mueller, Lukas A
The Tomato Expression Atlas
title The Tomato Expression Atlas
title_full The Tomato Expression Atlas
title_fullStr The Tomato Expression Atlas
title_full_unstemmed The Tomato Expression Atlas
title_short The Tomato Expression Atlas
title_sort tomato expression atlas
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860121/
https://www.ncbi.nlm.nih.gov/pubmed/28379331
http://dx.doi.org/10.1093/bioinformatics/btx190
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