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. 2017 Aug 1;33(15):2397-2398.
doi: 10.1093/bioinformatics/btx190.

The Tomato Expression Atlas

Noe Fernandez-Pozo  1 , Yi Zheng  1 , Stephen I Snyder  2 , Philippe Nicolas  1 , Yoshihito Shinozaki  2 , Zhangjun Fei  1   3 , Carmen Catala  1   2 , James J Giovannoni  1   3 , Jocelyn K C Rose  2 , Lukas A Mueller  1
Affiliations

The Tomato Expression Atlas

Noe Fernandez-Pozo et al. Bioinformatics. .

Abstract

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 .

Contact: jr286@cornell.edu or lam87@cornell.edu.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1
Fig. 1
The Tomato Expression Atlas cube (a) and expression images (b). Colors represent expression values in Reads Per Million (RPM)
See this image and copyright information in PMC

References

    1. Altschul S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403–410. - PubMed
    1. Fernandez-Pozo N. et al. (2015) The Sol Genomics Network (SGN)—from genotype to phenotype to breeding. Nucleic Acids Res., 43, D1036–D1041. - PMC - PubMed
    1. Martin L.B.B. et al. (2016) Laser microdissection of tomato fruit cell and tissue types for transcriptome profiling. Nat. Protoc., 11, 2376–2388. - PubMed
    1. Thimm O. et al. (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J., 37, 914–939. - PubMed
    1. Winter D. et al. (2007) An “Electronic Fluorescent Pictograph” browser for exploring and analyzing large-scale biological data sets. PLoS One, 2, e718.. - PMC - PubMed

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