VEnAS

VEnAS identifies genome-wide associations between enhancers and alternative splicing in human and mouse genomes to characterize enhancer-mediated regulation of transcript isoforms.

Key Features:

• Genome-wide Analysis: Integrates datasets from 28 human tissues/cell lines and 24 mouse tissues/cell lines to analyze enhancer–alternative splicing (AS) associations at genome scale.
• Data Integration and Statistical Analysis: Combines RNA-seq data with enhancer datasets and applies statistical methods to detect significant enhancer–AS associations across multiple tissues.
• Identification of Significant Associations: Reports 3,242 human genes and 7,716 mouse genes that exhibit significant enhancer–AS associations in at least one tissue.
• Quantitative Insights: Finds that approximately 6% of human enhancers and 5% of mouse enhancers are associated with changes in AS per gene, and that each enhancer is associated with about one gene in both species.
• Homologous Associations: Observes that 52% of significant human associations and 34% of significant mouse associations involve co-existence of homologous genes and enhancers, indicating evolutionary conservation.

Scientific Applications:

• Gene regulation: Enables investigation of enhancer-mediated regulation of alternative splicing to elucidate mechanisms controlling transcript isoform diversity.
• Evolutionary biology: Supports cross-species comparisons between human and mouse to study conservation of enhancer–AS relationships.
• Disease-related splicing research: Provides association data useful for exploring enhancer contributions to alternative splicing changes relevant to disease contexts.

Methodology:

Integration of RNA-seq data with enhancer datasets followed by application of statistical methods to identify significant enhancer–AS associations across tissues.