Stress-Response-Gene-Atlas/test

OsSRGA: an interactive web application to retrieve stress-responsive genes in Oryza sativa

Background

Abiotic and biotic stresses pose significant constraints to plant productivity. Elucidating the gene regulatory networks involved in plant stress responses and tolerance is essential for advancing future breeding programs and developing innovative agricultural products.

What is AtSRGA

We introduce OsSRGA (Oryza sativa Stress Responsive Gene Atlas), a user-friendly application enabling the retrieval of stress-responsive genes in Oryza sativa (Rice). The application was developed by collecting 1,131 microarray and 1,050 RNA sequencing datasets from publicly accessible databases. Those datasets corresponded to 11 biotic and abiotic stresses, including abscisic acid, cold, drought, heat, high light, hypoxia, osmotic stress, oxidation, salt, wounding, and Pseudomonas syringae pv. Tomato DC3000. Using a modified meta-analysis technique known as the vote-counting method, we computed integrated scores to evaluate the stress responsiveness for each stress condition across multiple studies. AtSRGA visualizes gene behavior under 11 stress conditions and offers an interactive, user-friendly interface accessible to researchers without bioinformatics training.

How To Use It

To run this App after downloading this App from Github to your local PC/Mac, please follow the steps as below:

1. 1.If 'Download ZIP', upzip the downloaded file (StressResponseGenesAtlas-main.zip) to the Desktop.

1. 1.Open R or RStudio (if installed) with R version >= 4.3.

1. 1.Set your working directory to where this App are unzipped or downloaded.

For example, I downloaded this App via 'Download ZIP' and unzipped it to the Desktop, then I need to set the working directory in R by setwd("~/Desktop/StressResponseGenesAtlas-main").

1. 1.Install all depended CRAN R packages and R Bioconductor packages by sourcing the R installation program with source("setup.R").

If all depended packages are successfully installed, logical value “TRUE” should be returned and printed on the R Console pane for each package after sourcing the installation program. Otherwise, please check whether you have the R version >=4.3 installed.

1. 1.Run this App by shiny::runApp()

1. 1.A web page will be open in your browser to show the stress-responsive gene atlas in rice. Tutorial files:
2. 2.English: AtSRGA tutorial
3. 3.Japanese (this repository): OsSRGA_tutorial_jp.pdf
4. 4.Japanese (Hugging Face direct link): OsSRGA_tutorial_jp.pdf

Feedback

If you have further questions or suggestions regarding this App, please contact Atsushi Fukushima at afukushima@kpu.ac.jp at the Kyoto Prefectural University (KPU).