HIPPIE

HIPPIE performs high-throughput analysis of Hi-C paired-end FASTQ reads to map DNA-DNA interactions and predict and characterize intra- and inter-chromosomal enhancer–target gene interactions.

Key Features:

• Workflow Integration: Integrates mapping of Hi-C paired-end FASTQ reads, quality control, and identification of DNA-DNA interacting fragments into a single analysis pipeline.
• Enhancer-Target Gene Prediction: Extracts and predicts relationships between enhancers and their target genes from Hi-C interaction data.
• High-Confidence Interaction Identification: Applies stringent quality control measures to identify high-confidence DNA-DNA interactions.
• Histone Modifications and DNase Hypersensitivity Detection: Detects histone modification and DNase hypersensitive enrichments to characterize putative enhancer elements.
• Computational Efficiency: Optimized for large datasets and for execution on high-performance computing clusters using Oracle Grid Engine.

Scientific Applications:

• Enhancer–target mapping: Identification of intra- and inter-chromosomal enhancer–target gene interactions from Hi-C data.
• Chromatin architecture analysis: Exploration of chromatin organization and DNA-DNA contact architecture relevant to gene expression regulation.
• Gene regulatory network and disease mechanism inference: Inference of gene regulatory relationships and investigation of mechanisms underlying biological processes and diseases via predicted enhancer-target links.

Methodology:

Mapping of raw Hi-C paired-end FASTQ reads; stringent quality control; identification of high-confidence DNA-DNA interacting fragments; characterization of putative enhancer elements via histone modification and DNase hypersensitivity analysis; extraction of potential enhancer-target gene interactions.