GURFAP

GURFAP provides gene function analysis for Glycyrrhiza uralensis (Leguminosae) by integrating whole-genome and transcriptomic data to support gene annotation, co-expression network construction, gene family prediction, and investigation of glycyrrhizin biosynthesis.

Key Features:

• Integration of Genomic and Transcriptomic Data: Leverages the whole-genome sequence of G. uralensis together with available transcriptomic data to construct gene co-expression networks for interpreting gene interactions.
• Gene Function Annotation: Annotates gene functions by aligning genomic data with public databases to produce evidence-based functional predictions.
• Gene Family Prediction: Predicts gene families using iTAK, HMMER, InParanoid, and PfamScan to identify transcription factors, protein kinases, and homologous gene groups.
• Comprehensive Analysis Tools: Provides sequence alignment and downstream analyses using BLAST, GSEA for gene set enrichment, Motif for motif discovery, Heatmap visualization, and JBrowse for genome browsing.
• Focus on Glycyrrhizin Biosynthesis: Identifies regulatory genes related to glycyrrhizin biosynthesis and highlights potential roles for MYB and bHLH transcription factors.
• Case Studies for Validation: Demonstrates platform application on glycyrrhizin pathway genes including CYP88D6, CYP72A154, and bAS.

Scientific Applications:

• Gene function discovery in G. uralensis: Enables identification and annotation of genes involved in licorice biology and secondary metabolism.
• Biosynthetic pathway analysis: Supports discovery of novel genes and regulatory factors in glycyrrhizin and other pharmacologically active compound pathways.
• Comparative and family-level analyses: Facilitates gene family classification and homolog identification across species using InParanoid and PfamScan.
• Gene regulation and network studies: Allows investigation of co-expression relationships and transcription factor involvement in pathway regulation.

Methodology:

Integrates whole-genome sequence and transcriptomic profiles, constructs gene co-expression networks, annotates genes by alignment to public databases, predicts gene families using iTAK, HMMER, InParanoid, and PfamScan, and applies BLAST, GSEA, Motif discovery, Heatmap visualization, and JBrowse for analysis.