DJExpress: An Integrated Application for Differential Splicing Analysis and Visualization.

Area of Science:

• Bioinformatics
• Genomics
• Computational Biology

Background:

• Alternative pre-mRNA splicing analysis from RNA-seq data offers deep insights into transcriptome complexity in health and disease.
• Existing bioinformatics pipelines for splicing analysis often require high computational power and specialized expertise, limiting accessibility for many researchers.
• Complex computational outputs and visualization challenges hinder the broader adoption of transcriptome-wide splicing analysis tools.

Purpose of the Study:

• Introduce DJExpress, an R package designed for user-friendly differential expression analysis of transcriptomic features and expression-trait associations.
• Enable researchers to determine gene-level differential junction usage and associations between junction expression and molecular/clinical features using raw splice junction counts.
• Provide an accessible tool that runs on average laptop computers with intuitive visualization formats for exploring alternative splicing alterations.

Main Methods:

• Utilizes raw splice junction counts as input for differential junction usage and expression-trait association analysis.
• Incorporates an R package, DJExpress, designed for ease of use on standard computational hardware.
• Features a web-compatible graphical interface for user data analysis and visualization within the differential junction expression in cancer (DJEC) database.

Main Results:

• DJExpress handles both annotated and de novo identified splice junctions, allowing the quantification of novel splicing events.
• The DJEC database integrates healthy, tumor, and cancer cell line junction expression data (TCGA, GTEx, DepMap).
• Integration with DepMap data enables association of junction expression with gene dependencies and drug response profiles, facilitating cancer model identification.

Conclusions:

• DJExpress provides a powerful and user-friendly solution for exploring alternative splicing alterations in RNA-seq data.
• The tool facilitates multi-level data integration, encompassing splicing signatures from healthy tissues, tumors, and cancer cell lines.
• DJExpress empowers broader research community engagement in alternative splicing analysis and its clinical/molecular implications.