PlantNexus

PlantNexus provides exploration and analysis of gene co-expression networks for barley (Hordeum vulgare) and sorghum (Sorghum bicolor) to support functional inference and characterization of regulatory mechanisms from RNA-seq data.

Key Features:

• Global Gene Co-expression Networks (GCNs): Global GCNs were constructed from 500 barley and 774 sorghum RNA-seq datasets to enable inference of putative gene functions and regulatory relationships via co-expression analysis.
• Tissue-Specific Networks: RNA-seq datasets are categorized into four tissue types—leaf, root, shoot, and flower/seed—to produce tissue-resolved GCNs.
• Network Visualization: Visualization of gene expression and co-expression relationships is provided at both global and tissue-specific levels to support network-level interpretation.
• Curated Meta-Information: Comprehensive meta-information is curated alongside RNA-seq datasets to supply contextual data for analyses.

Scientific Applications:

• Regulatory network analysis: Investigate regulatory networks underlying gene expression in barley and sorghum.
• Candidate gene identification: Identify candidate genes associated with specific traits or responses to environmental conditions using co-expression patterns.
• Comparative tissue studies: Compare gene expression and co-expression across leaf, root, shoot, and flower/seed to study developmental and tissue-specific processes.

Methodology:

Integration of large-scale RNA-seq datasets to construct robust GCNs for barley and sorghum (500 and 774 datasets, respectively) and curation and categorization of associated meta-information.