RoseAP

RoseAP provides functional annotation and co-expression network analysis of Rosa rugosa genes to support gene function discovery and pathway and regulatory analysis.

Key Features:

• Gene Annotation: Annotated 38,815 genes covering 97.76% of coding genes in Rosa rugosa with structural and functional annotations.
• Co-expression Network Construction: Constructed a co-expression network from 33 transcriptome samples (23 internal, 10 from the SRA database) using Pearson Correlation Coefficient (PCC) and Mutual Rank (MR), yielding approximately 29,657 positive and negative gene pairs representing 74.7% of coding genes.
• Functional Insights: Network analysis revealed relationships such as the connection between DFR and anthocyanin metabolism and identified genes with similar expression patterns, including several SAUR genes.
• Comprehensive Annotations: Provides Pfam domains, gene families, KEGG metabolic pathways, GO terms, InterPro annotation, trEMBL annotation, SwissProt annotation, and orthologues across 11 species for each gene.
• Auxiliary Analytical Tools: Includes BLAST, orthologue conversion, sequence extraction, expression value extraction, gene set enrichment analysis, and JBrowse for genome visualization.

Scientific Applications:

• Gene Function Discovery: Facilitates identification and characterization of gene functions in Rosa rugosa using integrated annotation and co-expression data.
• Pathway and Metabolic Analysis: Supports analysis of metabolic pathways such as anthocyanin biosynthesis through DFR-related network relationships.
• Comparative Genomics: Enables comparative analyses and orthologue mapping across 11 species using BLAST and orthologue conversion.
• Expression and Regulatory Network Analysis: Enables expression profiling and regulatory network analysis based on transcriptome-derived co-expression networks.

Methodology:

Gene annotation of 38,815 genes; co-expression network constructed from 33 transcriptome samples (23 internal, 10 from SRA) using Pearson Correlation Coefficient (PCC) and Mutual Rank (MR); annotations assigned via Pfam, KEGG, GO, InterPro, trEMBL, SwissProt and orthologue mapping across 11 species; auxiliary analyses include BLAST, orthologue conversion, sequence extraction, expression value extraction, gene set enrichment analysis, and visualization with JBrowse.