epiCOLOC

epiCOLOC performs context-dependent colocalization analysis of epigenomic features to interpret the functional relevance of genomic regions across human tissues and cell types.

Key Features:

• Extensive Epigenomic Data Integration: Integrates 44,385 bulk and single-cell epigenomic assays across 53 human tissues and cell types, including ChIP-seq, DNase-seq, and ATAC-seq profiling of transcription factor binding sites, histone modifications, open chromatin regions, and transcriptional events.
• Context-Dependent Analysis: Classifies epigenomic profiles into a hierarchical tissue and cell-type structure to enable context-aware colocalization analyses.
• Colocalization of User Queries: Performs colocalization analysis to determine whether user-defined genomic features are functionally related to reference epigenomic profiles.
• Biological Interpretation Support: Facilitates identification of underlying biological functions and relationships that characterize complex interactions between specified genomic regions and epigenomic features.

Scientific Applications:

• Interpretation of Disease-Associated Regions: Annotates and interprets disease- or trait-associated genomic regions by colocalizing them with epigenomic features across tissues and cell types.
• Identification of Regulatory Mechanisms: Identifies potential regulatory elements and transcriptional regulators by overlapping genomic queries with transcription factor binding, histone modification, and open chromatin datasets.
• Context-Aware Functional Annotation: Provides tissue- and cell-type–specific functional annotation of genomic loci using bulk and single-cell epigenomic evidence.

Methodology:

Integrates over 44,385 bulk and single-cell epigenomic assays from 53 human tissues/cell types, classifies profiles into a tissue/cell-type hierarchy, and computes colocalization between user-defined genomic queries and reference profiles derived from ChIP-seq, DNase-seq, and ATAC-seq.