Database: web application for visualization of the cumulated RNAseq data against the salicylic acid (SA) and methyl jasm
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Database: web application for visualization of the cumulated RNAseq data against the salicylic acid (SA) and methyl jasmonate (MeJA) treatment of Arabidopsis thaliana Dong U Woo1, Ho Hwi Jeon1, Halim Park1, Jin Hwa Park1, Yejin Lee1 and Yang Jae Kang1,2*
Abstract Background: Plants have adapted to survive under adverse conditions or exploit favorable conditions in response to their environment as sessile creatures. In a way of plant adaptation, plant hormones have been evolved to efficiently use limited resources. Plant hormones including auxin, jasmonic acid, salicylic acid, and ethylene have been studied to reveal their role in plant adaptation against their environment by phenotypic observation with experimental design such as mutation on hormone receptors and treatment / non-treatment of plant hormones along with other environmental conditions. With the development of Next Generation Sequencing (NGS) technology, it became possible to score the total gene expression of the sampled plants and estimate the degree of effect of plant hormones in gene expression. This allowed us to infer the signaling pathway through plant hormones, which greatly stimulated the study of functional genomics using mutants. Due to the continued development of NGS technology and analytical techniques, many plant hormone-related studies have produced and accumulated NGS-based data, especially RNAseq data have been stored in the sequence read archive represented by NCBI, EBI, and DDBJ. Description: Here, hormone treatment RNAseq data of Arabidopsis (Col0), wild-type genotype, were collected with mock, SA, and MeJA treatments. The genes affected by hormones were identified through a machine learning approach. The degree of expression of the affected gene was quantified, visualized in boxplot using d3 (datadriven-document), and the database was built by Django. Conclusion: Using this database, we created a web application (http://pgl.gnu.ac.kr/hormoneDB/) that lists hormone-related or hormone-affected genes and visualizes the boxplot of the gene expression of selected genes. This web application eventually aids the functional genomics researchers who want to gather the cases of the gene responses by the hormones. Keywords: Salicylic acid, Jasmonic acid, Web-application, Arabidopsis, RNAseq, Database
* Correspondence: [email protected] 1 Division of Bio & Medical Big data department (BK4 Program) at Gyeongsang National University, Jinju, Republic of Korea 2 Division of Life Science Department at Gyeongsang National University, Jinju, Republic of Korea © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Cr
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