MutRank

MutRank performs mutual rank (MR)-based coexpression analyses to identify coexpressed transcripts and predict functional associations in plant biology.

Key Features:

• Mutual Rank (MR)-Based Coexpression Analysis: Implements MR metrics to identify and quantify pairwise coexpression relationships among transcripts for functional association prediction.
• Exploratory and Targeted Analyses: Supports both unbiased exploratory MR analyses and hypothesis-driven targeted MR analyses of specified gene sets.
• Integration of Supporting Information: Incorporates user-provided supporting information to refine coexpression analyses and prioritize candidate genes.
• Pathway and Enzyme Prioritization: Uses MR-derived coexpression patterns to predict functional associations and narrow candidate pathway enzymes in biosynthetic and specialized metabolic pathways.
• Result Formats: Produces tabular and graphical coexpression results for downstream interpretation and analysis.

Scientific Applications:

• Gene function prediction: Rapidly identifies highly coexpressed transcripts to inform predictions of gene function and functional associations.
• Pathway discovery: Facilitates discovery and definition of biosynthetic and specialized metabolic pathways, including maize terpenoid antibiotic pathways.
• Candidate gene prioritization: Narrows candidate genes for biochemical pathway characterization and enzyme identification based on coexpression evidence.

Methodology:

Computes mutual rank (MR)-based coexpression metrics from expression data and integrates user-provided supporting information for exploratory and targeted analyses.