RgnTX

RgnTX performs colocalization analysis of transcriptomic elements while accounting for isoform heterogeneity and annotation ambiguity.

Key Features:

• Transcriptome-Specific Analysis: Leverages detailed transcriptome annotations to perform colocalization analysis specific to transcriptomic elements.
• Handling Isoform Heterogeneity and Ambiguity: Addresses isoform diversity and ambiguous isoform associations in input region sets.
• Flexible Null Model Simulation: Implements flexible null model simulations that represent transcriptome-wide backgrounds including alternative splicing patterns.
• Permutation Tests for Statistical Analysis: Uses permutation tests to assess colocalization significance while accommodating transcriptome variability.
• Pre-defined Computational Functions: Provides functions for visualization of permutation results, calculation of shifted z-scores, and multiple hypothesis testing using Benjamini-Hochberg correction.
• Comparative Performance: Produces more distinct and significant colocalization signals on synthetic and real datasets compared to genome-based methods.

Scientific Applications:

• Colocalization Analysis: Assessing spatial overlap and associations between transcriptomic region sets.
• Gene Regulation Studies: Investigating potential regulatory interactions and spatial relationships relevant to gene regulation.
• Alternative Splicing Analysis: Studying associations involving alternative splicing events and isoform-specific element distributions.
• Ambiguous Isoform Assignment Scenarios: Analyzing datasets where isoform associations are ambiguous due to technical constraints.

Methodology:

Performs permutation testing with flexible null model simulations that use transcriptome annotations and alternative splicing patterns, computes shifted z-scores, and applies Benjamini-Hochberg correction for multiple hypothesis testing.