CAGExploreR

CAGExploreR analyzes transcription start site (TSS) usage within promoter regions as an R package, detecting shifts in TSS utilization across Cap Analysis Gene Expression (CAGE) libraries to study promoter-driven transcript isoform variation and regulatory network changes.

Key Features:

• Detection of TSS shifts: Detects shifts in TSS utilization within broader promoter regions to identify alternative promoter activity.
• Comparative visualization: Provides comparative visualization of TSS and promoter usage across experimental conditions or cell types.
• Multi-sample CAGE integration: Integrates and compares multiple Cap Analysis Gene Expression (CAGE) libraries for multi-sample analyses.
• Promoter database integration and custom regions: Uses promoter definitions from FANTOM5 and MPromDb and accepts custom-defined regions for tailored analyses.
• Inference of isoform and regulatory effects: Produces analyses that inform transcript isoform generation and regulatory network modifications driven by alternative promoter usage.

Scientific Applications:

• Gene expression regulation: Analysis of promoter usage and TSS dynamics to study mechanisms of gene expression regulation.
• Transcriptomics and isoform diversity: Investigation of how alternative promoter usage contributes to RNA and protein diversity via transcript isoform variation.
• Comparative studies: Comparative analysis of promoter and TSS changes across cell types, developmental stages, or experimental conditions.
• Promoter annotation and validation: Cross-referencing CAGE-derived promoter activity with FANTOM5 and MPromDb annotations to validate or refine promoter definitions.

Methodology:

Sensitive quantification of TSS usage across integrated Cap Analysis Gene Expression (CAGE) libraries and comparative visualization to detect shifts in TSS utilization within specified promoter regions.