Hi-C Aggregate

Hi-C Aggregate constructs high-density, species-specific genome-wide chromatin contact maps by meta-analytically aggregating Hi-C experiments from human, mouse, and fly to capture long-range and trans-chromosomal interactions.

Key Features:

• High-Resolution Mapping: Aggregates thousands of Hi-C datasets to produce dense chromatin interaction maps that mitigate sparsity at increased genomic distances.
• Enhanced Predictive Power: Meta-Hi-C networks improve prediction of long-range coexpression and expression quantitative trait loci (eQTLs) relative to individual Hi-C datasets, with median AUC scores of 0.65 for cis interactions and 0.64 for trans interactions.
• Functional Insight: Captures functional chromatin contacts across both cis and trans configurations, enabling detection of regulatory relationships not explained by linear genomic distance alone.
• Cross-Species Analysis: Enables assessment of chromatin contact conservation between species and associates conserved contacts with coexpression, including in species lacking Hi-C data.
• Comprehensive Integration: Provides an aggregated network resource that complements other analytical approaches aimed at improving specificity or interpretation of chromatin interactions.

Scientific Applications:

• Gene Expression Regulation: Elucidates long-range and trans-chromosomal relationships relevant to regulation of gene expression.
• eQTL Analysis: Supports identification and interpretation of expression quantitative trait loci by providing aggregated chromatin contact evidence.
• Evolutionary Biology: Facilitates analysis of chromatin contact conservation to inform evolutionary and comparative functional genomics.

Methodology:

Aggregates 3,600 human, 6,700 mouse, and 500 fly Hi-C experiments via a meta-analytic approach to build species-specific meta-Hi-C contact maps (304 billion, 193 billion, and 19 billion contacts respectively) and evaluates predictive performance using median AUC for cis (0.65) and trans (0.64) interactions.