NetREx

NetREx constructs ranked tissue-specific co-expression networks from RNA sequencing data to characterize gene interactions and stress-response mechanisms in rice under drought, flood, cold, osmotic stress and hormonal treatments (abscisic acid and jasmonic acid).

Key Features:

• Ranked co-expression networks: Hosts co-expression networks derived from uniform experimental conditions, ranked to enable comparison of gene interactions under drought, flood, cold, osmotic stress, and abscisic acid and jasmonic acid treatments.
• Gene query and analysis modules: Implements modules to query genes across root and shoot tissues and to examine expression changes, module memberships, and associated pathways.
• Subnetwork analysis: Enables definition of subnetworks within tissue-specific networks to investigate fold change, gene annotations, and neighborhood interactions of specified genes.
• Orthologous gene querying: Supports querying of orthologous genes in Arabidopsis, wheat, maize, barley, and sorghum for comparative genomic analyses.

Scientific Applications:

• Candidate gene identification: Identifies novel candidate genes associated with stress responses using ranked co-expression and subnetwork analyses.
• Tissue-specific stress-response analysis: Elucidates tissue-specific interactions in root and shoot under drought, flood, cold, osmotic stress, and abscisic acid and jasmonic acid treatments in rice.
• Comparative genomics: Facilitates cross-species comparison of gene function and conservation through ortholog queries in Arabidopsis, wheat, maize, barley, and sorghum.
• Crop resilience research: Analyzes gene expression patterns and molecular mechanisms underlying stress responses to inform strategies for enhancing rice resilience to environmental stresses.

Methodology:

Utilizes publicly available RNA sequencing data with molecular hierarchy annotations to construct and rank co-expression networks, analyzed under uniform experimental conditions.