The Tomato Expression Atlas

• Published in: Bioinformatics (Oxford, England) Vol. 33; no. 15; pp. 2397 - 2398
• Main Authors: 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
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.08.2017
• Subjects: Applications Notes; Databases, Nucleic Acid; Gene Expression Regulation, Plant; High-Throughput Nucleotide Sequencing; Lycopersicon esculentum - genetics; Organ Specificity; Sequence Analysis, RNA - methods; Transcriptome
• ISSN: 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btx190

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. The Tomato Expression Atlas is available at http://tea.solgenomics.net/ . Source code is available at https://github.com/solgenomics/Tea . jr286@cornell.edu or lam87@cornell.edu. Supplementary data are available at Bioinformatics online.