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Loop Catalog: a comprehensive HiChIP database of human and mouse samples
Joaquin Reyna1,2, Kyra Fetter1,3, Romeo Ignacio1,4
1Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA.
Genome Biology
|June 20, 2025
Summary
Loop Catalog is a new database that makes it easy to find and analyze chromatin loops from HiChIP and Hi-C data. It helps researchers interpret genetic variants and understand gene regulation.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- High-throughput chromatin interaction capture (HiChIP) provides high-resolution chromatin loop profiling.
- An increasing volume of HiChIP data necessitates centralized resources for analysis.
Purpose of the Study:
- To develop Loop Catalog, a web-based database for HiChIP and Hi-C loop calls.
- To provide a comprehensive resource for exploring and analyzing chromatin interaction data.
Main Methods:
- Aggregated loop calls from over 1000 human and mouse HiChIP samples and 44 Hi-C samples.
- Integrated analysis modules for SNP-to-gene linking, motif analysis, and network generation.
Main Results:
- The catalog contains over 4.19 million unique chromatin loops.
- Demonstrated utility in interpreting GWAS and eQTL variants.
- Facilitated identification of regulatory networks and sequence motifs.
Conclusions:
- Loop Catalog is a valuable resource for the genomics community.
- Enables deeper understanding of chromatin structure and gene regulation.
- Supports interpretation of genetic variants in the context of 3D genome organization.
