CASA

CASA compiles and annotates alternative splicing (AS) events from RNA-seq datasets to characterize host splicing alterations in COVID-19 and other infectious diseases.

Key Features:

• Extensive Data Repository: Aggregates RNA-seq datasets from 65 different tissues, organoids, and cell lines to enable quantitative analysis of AS across diverse conditions.
• Detection and Visualization: Identified 262,994 AS events associated with infectious diseases and provides visual representations of splicing patterns across microbial infections.
• Functional Annotation Analysis: Links dynamic AS events to functional annotations to assess potential biological impacts.
• Drug-Target Interaction Exploration: Maps AS-affected transcripts to drug-target interaction data to highlight potential therapeutic relevance.
• RNA-Binding Protein (RBP) Data: Incorporates RNA-binding protein information that potentially regulates dynamic AS events.
• Cross-Virus Comparative Analysis: Enables comparison of microbe-induced host splicing changes across different virus families to identify condition-specific patterns.

Scientific Applications:

• Immune-response and host-pathogen interaction studies: Investigates how alternative splicing modulates immune responses and host-virus interactions during infection.
• Translational research and therapeutic targeting: Supports prioritization of AS events and AS-affected drug-target interactions for therapeutic hypothesis generation.
• RBP regulatory mechanism discovery: Facilitates identification of RNA-binding proteins potentially regulating infection-induced AS changes.
• Comparative virology of splicing responses: Enables cross-virus analyses to detect shared and virus-specific splicing alterations.

Methodology:

Developed through rigorous reanalysis of thousands of RNA-seq datasets with a systematic approach to data integration and visualization to identify and characterize AS events.