C3D

C3D predicts three-dimensional genomic interactions between cis-regulatory elements and gene promoters by leveraging correlations in DNaseI hypersensitivity across cell types.

Key Features:

• Unsupervised algorithm: Employs an unsupervised method that leverages correlations in DNaseI hypersensitivity signals to predict chromatin interactions without labeled training data.
• Cross cell-type correlation: Analyzes and predicts interactions across different cell types by utilizing cross-cell-type correlation strategies.
• Validation with ChIA-PET: Demonstrated overlap with ChIA-PET interactions, identifying 32.7% of promoter–distal DHS interactions in K562, 18.3% in MCF-7, and 24.1% in GM12878.

Scientific Applications:

• Gene regulation inference: Infers regulatory connections between distal cis-regulatory elements and gene promoters to inform gene regulation studies.
• Chromatin architecture analysis: Supports investigation of three-dimensional genome organization and chromatin interactions.
• Cross-cell-type regulatory comparison: Enables comparative analysis of regulatory interactions across multiple cell types.

Methodology:

Uses DNaseI hypersensitivity data as the primary input; implemented in Bash and R with required software versions Bash (≥4.0), R (≥3.1.1), and BEDTools (≥2.19.0); utilizes R packages GenomicRanges, Sushi, data.table, preprocessCore, and dynamicTreeCut.