HpeNet

HpeNet provides a co-expression network database and transcriptome-derived gene annotations to support functional genomics and lipid metabolism (including α-linolenic acid biosynthesis) research in Paeonia lactiflora Pall.

Key Features:

• RNA-seq datasets: Includes 40 RNA-seq datasets generated from ten different tissues of Paeonia lactiflora Pall. cv Shaoyou17C.
• De novo transcriptome assembly: Produced a collection of 416,062 unigenes from the assembled transcriptomes.
• Homology annotation: Approximately 57% (236,222) of unigenes were matched to sequences in public databases via homology searches.
• Co-expression network: A co-expression network encompassing 95.13% of identified unigenes to support gene relationship inference.
• Functional prediction: Integration of transcriptome data and co-expression relationships to improve gene annotation and functional inference for a species without a reference genome.
• Analytical tools: Supports BLAST searches, gene expression profiling analysis, and Gene Set Enrichment Analysis (GSEA).
• Lipid metabolism focus: Enables analysis of lipid metabolism pathways, including genes implicated in α-linolenic acid biosynthesis.
• Orthology information: Provides orthologous matches derived from homology searches to assist comparative analyses.

Scientific Applications:

• Gene function prediction: Use co-expression and homology data to infer functions of unigenes in Paeonia lactiflora Pall.
• Lipid metabolism research: Investigate genes and pathways involved in lipid biosynthesis and α-linolenic acid accumulation.
• Tissue-specific expression analysis: Perform gene expression profiling across ten tissues to identify tissue-enriched transcripts.
• Gene set enrichment: Apply GSEA to identify enriched pathways or functional categories from expression data.
• Comparative genomics: Leverage orthologous matches for cross-species comparison and annotation transfer.

Methodology:

Processing included generation of 40 RNA-seq datasets from ten tissues of Paeonia lactiflora Pall. cv Shaoyou17C, de novo transcriptome assembly yielding 416,062 unigenes, homology searches annotating ~236,222 unigenes (~57%), construction of a co-expression network covering 95.13% of unigenes, and provision of BLAST, gene expression profiling, and GSEA analyses.