WheatCENet

WheatCENet constructs and compares co-expression networks across allohexaploid wheat and its diploid and tetraploid progenitors using extensive transcriptome data to identify functional gene modules.

Key Features:

• Comparative Network Construction: Constructs co-expression networks for diploid, tetraploid, and hexaploid wheat species from extensive transcriptome data and enables direct comparison across ploidy levels.
• Functional Annotation Integration: Integrates pathways, gene families, protein–protein interactions, microRNAs (miRNAs), and epigenome data into the co-expression networks.
• Analytical Tools: Provides Gene Ontology (GO) annotation, gene set enrichment analysis (GSEA), and motif identification for functional interrogation of network modules.
• Transcriptome-driven Inference: Uses extensive transcriptome datasets as the basis for network inference across wheat species.

Scientific Applications:

• Polyploidization Analysis: Dissects genetic and epigenetic changes associated with polyploidization by comparing co-expression networks across allohexaploid, tetraploid, and diploid wheat.
• Functional Module Identification: Identifies gene functions clustered within co-expression modules and supports functional interpretation via GO and GSEA.
• Evolutionary and Regulatory Discovery: Enabled identification of a novel CCarG motif in the promoter of WAPO-A1, implicating neofunctionalization affecting spikelet development in hexaploid wheat.

Methodology:

Constructs co-expression networks from transcriptome data, performs comparative co-expression network analysis across ploidy levels, integrates pathway, gene family, protein–protein interaction, miRNA, and epigenome annotations, and applies GO annotation, GSEA, and motif identification.