SoyFN

SoyFN provides soybean-specific gene and microRNA functional networks for omics-level analysis of gene-gene, gene-miRNA, and miRNA-miRNA interactions.

Key Features:

• Functional network representations: Generation and analysis of soybean gene and miRNA networks encompassing gene-gene, gene-miRNA, and miRNA-miRNA associations.
• Integration with omics data: Incorporation of KEGG pathways, gene ontology annotations, and 3'-UTR sequences to contextualize network relationships.
• Analytical tools: Includes SoySearch, ID mapping, Genome Browser, eFP Browser, and promoter motif scan for querying, identifier conversion, genomic context visualization, expression analysis, and regulatory element identification.

Scientific Applications:

• Gene function prediction: Use of network topology and gene-miRNA associations to infer gene functions and regulatory mechanisms.
• Pathway analysis: Mapping network components to KEGG pathways to identify metabolic and signaling pathways relevant to soybean development and stress responses.
• Genomic and expression studies: Relating network interactions to genomic loci and expression patterns using Genome Browser and eFP Browser.

Methodology:

Construction of gene-gene, gene-miRNA, and miRNA-miRNA functional networks from integrated omics datasets including KEGG, gene ontology, and 3'-UTR sequence information.