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

Sanchari Sircar, Mayank Musaddi¹, Nita Parekh¹

¹Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Gachibowli, Hyderabad 500032, India.

Database : the Journal of Biological Databases and Curation

|August 6, 2022

Summary

This summary is machine-generated.

NetREx is a new server for analyzing rice gene expression networks. It helps researchers find new genes involved in plant stress responses, aiding crop improvement for climate change adaptation.

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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.