InterTADs

InterTADs integrates multi-omics datasets such as DNA methylation, gene expression, and mutation data within topologically associating domains (TADs) to contextualize genomic events by chromatin architecture.

Key Features:

• Integration Framework: Constructs a unified matrix of genomic events that includes coordinates and quantitative metrics scaled for comparability across omics types.
• Topological Contextualization: Partitions integrated data by TADs based on chromosomal locations to evaluate events in their chromatin context.
• Statistical Analysis: Performs statistical evaluation within each TAD to identify significant differences between groups (e.g., normal vs. cancer).
• Visualization Capabilities: Maps events onto chromosomal locations within TADs and visualizes distributions of event counts across study groups.

Scientific Applications:

• Multi-omics contextualization in life sciences: Enables discovery of associations across DNA methylation, gene expression, and mutation data when analyzed within TADs.
• Cancer genomics: Supports detection and interpretation of spatially organized genomic alterations relevant to cancer.

Methodology:

Implemented in R, InterTADs builds a unified, scaled matrix of genomic events with coordinates, divides the integrated data by TADs using chromosomal locations, conducts statistical comparisons within each TAD between groups, and generates mappings of events onto chromosomes and distributions of event counts.