NetREx: Network-based Rice Expression Analysis Server for abiotic stress conditions.

Area of Science:

• Plant genomics and bioinformatics
• Transcriptomics and gene expression analysis
• Agricultural science and climate change adaptation

Background:

• Transcriptomic studies in crops like rice, wheat, and maize offer insights into agriculture and climate change.
• Re-analyzing public transcriptomic data with molecular annotations can greatly benefit plant research.
• Co-expression networks are crucial for understanding gene coordination in biological processes.

Purpose of the Study:

• To develop NetREx, a Network-based Rice Expression Analysis Server.
• To host ranked co-expression networks for Oryza sativa using public RNA sequencing data.
• To provide tools for analyzing gene expression across various stress conditions, hormonal treatments, and tissues.

Main Methods:

• Developed NetREx, a web server hosting ranked co-expression networks for rice (Oryza sativa).
• Utilized publicly available messenger RNA sequencing data under uniform experimental conditions.
• Integrated interactable data viewers for analyzing user-queried genes, subnetworks, and orthologous genes.

Main Results:

• NetREx provides access to gene co-expression networks across different stress conditions (drought, flood, cold, osmosis) and treatments.
• Users can query subnetworks, view fold changes, gene annotations, and analyze neighboring genes and pathways.
• The server facilitates querying orthologous genes from Arabidopsis, wheat, maize, barley, and sorghum.

Conclusions:

• NetREx aids in identifying novel candidate genes and tissue-specific interactions under stress.
• The server assists in analyzing and understanding complex phenotypes related to stress response in rice.
• NetREx supports plant research community in leveraging transcriptomic data for crop improvement and climate resilience.