iDJExpress

iDJExpress performs differential junction expression analysis of RNA-seq data to quantify annotated and de novo splice junctions and relate alternative pre-mRNA splicing events to molecular features from TCGA, GTEx, and DepMap.

Key Features:

• R implementation: Provided as an R package for computational analysis of splice junction expression and differential junction usage.
• Differential expression analysis: Performs differential expression testing of transcriptomic features with emphasis on alternative pre-mRNA splicing events.
• Raw splice junction input: Accepts raw splice junction counts and processes both annotated and de novo identified junctions.
• Novel junction quantification: Quantifies novel splice events derived from de novo junction calls alongside annotated junctions.
• Visualization functions: Provides visualization routines for splice junction expression and differential junction usage.
• DJEC DB integration: Integrates with the DJEC DB containing junction expression data from healthy and tumor tissues sourced from TCGA and GTEx and cancer cell line data from DepMap.
• Functional genomics integration: Incorporates DepMap functional genomics datasets to associate junction expression with gene dependencies and drug response profiles.

Scientific Applications:

• Alternative splicing profiling: Analysis of alternative splicing alterations across healthy tissues, tumors, and cancer cell lines using RNA-seq junction counts.
• Novel splice discovery: Detection and quantification of de novo splice junctions to expand annotated transcriptome catalogs.
• Splicing–phenotype associations: Linking differential junction expression to molecular features such as gene dependencies and drug response profiles.
• Model selection for experimental follow-up: Identification of cancer cell models with specific splicing alterations using integrated TCGA, GTEx, and DepMap data.

Methodology:

Implemented in R; accepts raw splice junction counts; performs differential junction expression analysis focused on alternative pre-mRNA splicing; processes annotated and de novo junctions and quantifies novel splice events; integrates DJEC DB, TCGA, GTEx, and DepMap datasets and computes associations between junction expression and molecular features such as gene dependencies and drug response profiles.