StCoExpNet

StCoExpNet provides a global expression atlas and co-expression network for Solanum tuberosum L. to identify genes associated with agronomic traits and tissue-specific transcriptional patterns.

Key Features:

• Global expression atlas: Constructed from 2,299 publicly accessible transcriptome samples spanning 15 tissues to represent gene activity across potato tissues.
• Genome-wide expression coverage: Reports that approximately 87% of annotated genes show detectable expression in at least one sample.
• Housekeeping gene identification: Detects 281 housekeeping genes characterized by consistent and stable expression across samples.
• Tissue-specific gene identification: Identifies 308 genes with marked tissue-specific expression patterns.
• Co-expression network analysis: Builds a global co-expression network that identifies clusters of co-expressed genes and links clusters to agronomic traits such as self-incompatibility, anthocyanin biosynthesis, tuberization, and defense against pathogens.

Scientific Applications:

• Tissue-resolved gene expression profiling: Enables characterization of gene expression patterns across 15 potato tissues.
• Candidate gene discovery for agronomic traits: Supports identification of genes and co-expression modules associated with self-incompatibility, anthocyanin biosynthesis, tuberization, and pathogen defense.
• Reference set of constitutive and specific genes: Provides lists of housekeeping and tissue-specific genes for functional studies and comparative analyses.
• Potato genetics and genomics research: Facilitates investigations into transcriptional complexity and the genetic basis of important biological processes in potatoes.

Methodology:

Integration of transcriptome data from publicly available sources to construct a global expression atlas from 2,299 samples across 15 tissues, analysis to identify housekeeping and tissue-specific genes, and construction of a global co-expression network to link gene clusters to agronomic traits.