AtFusionDB

AtFusionDB catalogs fusion transcripts in Arabidopsis thaliana, providing a repository of chimeric RNAs and associated annotations for analysis.

Key Features:

• Dataset scope: Contains 82,969 fusion transcript entries derived from 17,181 distinct genes.
• Annotation fields: Records Ensembl gene names, official gene names, tissue types, fusion type, AtFusionDB ID, and Sequence Read Archive (SRA) sample IDs.
• Significance metric: Provides EricScore as a metric for evaluating the significance of fusions.
• Identifiers and coordinates: Includes UniProt identifiers and genomic coordinates with parental gene functions.
• Junction sequences: Stores junction sequences for each fusion transcript entry.
• Expression data: Reports expression levels for both parental genes and the fusion transcript.
• Sequence analysis modules: Supports BLASTN, SW Align, and Mapping for sequence alignment and mapping against database entries.

Scientific Applications:

• Fusion discovery and annotation: Enables identification and cataloging of chimeric RNAs in Arabidopsis thaliana.
• Functional genomics: Facilitates studies of gene function and the potential impact of fusion transcripts.
• Expression analysis: Supports comparative analysis of parental gene and fusion transcript expression levels.
• Comparative and alignment-based studies: Enables sequence mapping and alignment for comparative genomic analyses.

Methodology:

Computational methods explicitly include BLASTN, SW Align, Mapping modules and the EricScore metric; entries are linked to Sequence Read Archive (SRA) sample IDs.