HiSIF

HiSIF identifies significant chromatin interactions from Hi-C data, focusing on promoter-distal loops to link chromatin architecture with gene regulation.

Key Features:

• Genome-wide interacting loci identification: Pinpoints specific interacting loci across the genome rather than megabase-size domains.
• Promoter-distal loop detection: Targets promoter-distal loops to uncover functional relationships between chromatin structure and gene regulation.
• Loop detection via CERN ROOT: Uses the standalone CERN ROOT C++ framework to extract fit parameters of cis-trans interactions and has been demonstrated to outperform existing tools in loop identification.
• Protocol support: Supports Hi-C, TCC (Transcription-Associated Chromosome Conformation Capture), and in situ Hi-C experimental protocols.
• Data preprocessing: Includes a small C tool to process initial sequencing data from the NCBI database.
• Implementation and requirements: Implemented in C++/C, leverages parallel processing, and operates on Linux requiring the g++ compiler and reference genome HG19.

Scientific Applications:

• Chromatin interaction mapping: Maps genome-wide chromatin interactions and promoter-distal loops to study links between chromatin architecture and gene regulation.
• Cancer genomics and prognostic marker discovery: Applied to breast cancer Hi-C data to identify 21 genes with gained loops that correlated with worse relapse-free survival in endocrine-treated patients, indicating potential prognostic markers.

Methodology:

Extracts fit parameters of cis-trans interactions using the CERN ROOT C++ framework; implemented in C/C++ with parallel processing; includes a small C tool for initial NCBI data processing and requires g++ and reference genome HG19 on Linux.