InTAD

InTAD is an R/Bioconductor package for identifying enhancer–gene regulatory relationships by integrating gene expression data with epigenomic signals (e.g., enhancer activity derived from ChIP-seq assays) in the context of 3D chromatin organization. The method leverages the observation that enhancers and their target genes frequently reside within the same topologically associated domain (TAD), a structural unit of chromatin defined by Hi-C and other chromosome conformation capture technologies. By restricting statistical testing to enhancer–gene pairs located within shared TADs or chromatin loop anchors, InTAD reduces the multiple-testing burden and increases the biological relevance of inferred associations.

For each enhancer–gene pair, InTAD evaluates correlations of expression across a heterogeneous cohort of samples, identifying both proximal and distal regulatory relationships not apparent from linear genome proximity alone. Users may incorporate publicly available TAD boundary annotations or supply custom domain definitions, allowing integration with diverse assays and experimental designs. The package provides flexible parameterization for exploring the influence of covariates, alternative correlation measures, and filtering strategies, and offers a suite of visualization tools to inspect enhancer–gene links, correlation patterns, and genomic context.

InTAD enables systematic discovery of putative regulatory interactions in studies combining transcriptomic and epigenomic profiling, and has been validated on enhancer–expression datasets from ependymoma tumors. Because it is applicable to any multi-sample dataset containing matched gene expression and enhancer-associated signals, InTAD provides a robust framework for characterizing regulatory circuitry within TADs and interpreting cell-type-specific epigenomic activity in the context of 3D genome architecture.