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MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with
Elly Poretsky1, Alisa Huffaker1
1Division of Biology, University of California, San Diego, La Jolla, CA, USA.
Peerj
|November 26, 2020
Summary
We developed MutRank, an R Shiny web application, to accelerate the discovery of plant specialized metabolite pathways by analyzing gene coexpression. This tool aids in predicting gene functions and associations, speeding up biological discoveries.
Area of Science:
- Plant Biology
- Biochemistry
- Bioinformatics
Background:
- Assigning genotypes to phenotypes is challenging.
- Gene clusters accelerate specialized metabolite pathway discovery, but genes are often dispersed or uninformative.
- Gene co-regulation in transcript abundance is a reliable indicator for pathway gene identification.
Purpose of the Study:
- To develop a user-friendly web application for flexible Mutual Rank (MR)-based coexpression analyses.
- To facilitate rapid hypothesis testing and gene function prediction for plant specialized metabolites.
- To accelerate the discovery of novel biosynthetic pathways.
Main Methods:
- Developed MutRank, an R Shiny web application for coexpression analyses.
- Integrated user-provided data with customizable features for hypothesis testing.
- Utilized Mutual Rank (MR)-based coexpression analyses to identify functional associations.
Main Results:
- MutRank provides an intuitive interface for analyzing coexpression data.
- The tool accelerates gene function predictions and pathway discoveries.
- Demonstrated utility in defining two maize terpenoid antibiotic pathways.
Conclusions:
- MutRank simplifies and speeds up coexpression analyses for plant biology research.
- The application supports unbiased and user-defined coexpression analyses.
- MutRank is a valuable tool for predicting gene functions and discovering biosynthetic pathways.
