PFusionDB

PFusionDB compiles plant-specific fusion transcripts from RNA-Seq data across multiple species to support research into fusion transcript formation in plants.

Key Features:

• Species Coverage: Contains fusion transcript data for Arabidopsis thaliana, Oryza sativa japonica, Oryza sativa indica, and Cicer arietinum.
• Fusion Transcript Catalog: Repositories include 80,170, 39,108, 83,330, and 11,500 unique fusions detected in 1,280, 637, 697, and 181 RNA-Seq samples respectively.
• Non-recurrent Fusion Annotation: Documents 76,599, 35,480, 72,099, and 9,524 non-recurrent fusion transcripts found in only one sample for each species.
• Fusion Event Metadata: Provides parental gene information, junction sequence, expression levels, breakpoint coordinates, strand information, tissue type, treatment information, fusion type, PFusionDB ID, and Sequence Read Archive ID.
• Sequence Search Modules: Includes BLASTN, SW Align, and Mapping modules for query sequence mapping and alignment to fusion transcripts.

Scientific Applications:

• Plant Fusion Transcript Research: Serves as a foundational resource for investigating fusion transcript biology in plant systems, an area relatively understudied compared to cancer biomarker research.
• Comparative Fusion Analysis: Enables cross-species examination of fusion transcript patterns across dicot and monocot model organisms and crop species.
• Recurrence and Expression Studies: Supports analysis of fusion transcript recurrence rates and expression characteristics in diverse plant tissues and conditions.

Methodology:

Fusion transcript identification was performed using five tools: EricScript-Plants, STAR-Fusion, TrinityFusion, SQUID, and MapSplice.