ccnWheat

ccnWheat constructs and compares co-expression networks from wheat transcriptome data to investigate gene expression and regulatory network changes across diploid, tetraploid, and hexaploid wheat.

Key Features:

• Network Construction: Constructs co-expression networks for diploid, tetraploid, and hexaploid wheat species to enable comparative analyses.
• Functional Annotations Integration: Integrates pathways, gene families, protein-protein interactions, microRNAs (miRNAs), and epigenome data.
• Analytical Tools: Provides Gene Ontology (GO) annotation, gene set enrichment analysis (GSEA), motif identification, and related analytical functions.
• Comparative Analysis: Searches and compares specific functional co-expression networks to identify related gene functions within clusters.

Scientific Applications:

• Gene Function Exploration: Examines differential co-expression of genes such as WHEAT ABERRANT PANICLE ORGANIZATION 1 (WAPO1) between hexaploid wheat and progenitors to study spike development.
• Motif Identification: Identifies motifs such as a CCarG motif in the promoter of WAPO-A1, suggesting neofunctionalization affecting spikelet development.
• Polyploidization Studies: Investigates genetic and epigenetic changes following polyploidization that lead to variable gene expression and altered regulatory networks.

Methodology:

Builds and compares co-expression networks from large-scale transcriptome data and integrates functional annotations to support GO, GSEA, motif analyses, and comparative network searches across diploid, tetraploid, and hexaploid wheat.