PAGER (Pattern Analysis of Gene Expression in Root) is a pipeline designed to analyse and visualize gene and reporter expression patterns in root.
PAGER work with data coming from the CellSet image analysis tool and is based on the Root System Markup Language (RSML).
PAGER perfoms two main analysis: 1. A pair-wise comparison for reporter flourescence levels for each combinaison of reporter lines. For each combinaison, PAGER perfoms a MANOVA analysis and computes an r-square, Pearson and Spearman (ranked) correlation factors. 2. A pair-wise comparison of the reporter fluorescence levels data and expression data (microarray) for each line. For each combinaison, PAGER computes an r-square, Pearson and Spearman (ranked) correlation factors.
PAGER has been developed as a Shiny app, to ease its maintenance and deployment. If you want to try the app, with sample data, try the online version:
Or, if you want to use your own data, launch it from your own computer: 1. Install R (if you do not have the latest version of R, it will help to update it) 2. (Optional) Install RStudio 3. Open R and, in the console, type in the following code:
install.packages("shiny")
library("shiny")
shiny::runGitHub("PAGERoot/PAGER-Shiny", "PAGERoot")
PAGER will open, either in a new window if you are using RStudio, or in your favorite web browser.
PAGER requires two types of datafiles to run: 1. An RSML file that contains the fluoresence data 2. A datafile (.csv) that contains the gene expression data For each of these files, the data needs to be organised by cell types. The types allowed are : - Columella - Stele - Cortex - Quiecent center - Endodermis - Exodermis - Lateral root cap View user manual
PAGER was build to work with data store in a Root System Markup Language (RSML) file.
The RSML format was indeed created as common format for storing root system information, and accomodates well for the storage of fluoresence data.
PAGER what born from a collaboration between researchers from the Carnegie Science Institute (José Dinneny) and the Forschungszentrum Juelich (Guillaume Lobet). PAGER what first used here:
A synthetic biology pipeline identifies a common regulatory mechanism between stress and development in roots Rui Wu, Lina Duan, José Pruneda-Paz, Guillaume Lobet, Shahram Emami, Dong-ha Oh, Micheal Pound, Jonah Kornbluh, Muh-ching Yee, Steve Kay, and José R. Dinneny
