Loop Catalog: a comprehensive HiChIP database of human and mouse samples
Abstract HiChIP enables cost-effective and high-resolution profiling of chromatin loops. To leverage the increasing number of HiChIP datasets, we develop Loop Catalog ( https://loopcatalog.lji.org ), a web-based database featuring loop calls from over 1000 distinct human and mouse HiChIP samples fro...
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| Format: | Article |
| Language: | English |
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BMC
2025-06-01
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| Series: | Genome Biology |
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| Online Access: | https://doi.org/10.1186/s13059-025-03615-5 |
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| author | Joaquin Reyna Kyra Fetter Romeo Ignacio Cemil Can Ali Marandi Astoria Ma Nikhil Rao Zichen Jiang Daniela Salgado Figueroa Sourya Bhattacharyya Ferhat Ay |
| author_facet | Joaquin Reyna Kyra Fetter Romeo Ignacio Cemil Can Ali Marandi Astoria Ma Nikhil Rao Zichen Jiang Daniela Salgado Figueroa Sourya Bhattacharyya Ferhat Ay |
| author_sort | Joaquin Reyna |
| collection | DOAJ |
| description | Abstract HiChIP enables cost-effective and high-resolution profiling of chromatin loops. To leverage the increasing number of HiChIP datasets, we develop Loop Catalog ( https://loopcatalog.lji.org ), a web-based database featuring loop calls from over 1000 distinct human and mouse HiChIP samples from 152 studies plus 44 high-resolution Hi-C samples. We demonstrate its utility for interpreting GWAS and eQTL variants through SNP-to-gene linking, identifying enriched sequence motifs and motif pairs, and generating regulatory networks and 2D representations of chromatin structure. Our catalog spans more than 4.19M unique loops, and with embedded analysis modules, constitutes an important resource for the field. |
| format | Article |
| id | doaj-art-7b581504151b473abb738d79b797f96d |
| institution | DOAJ |
| issn | 1474-760X |
| language | English |
| publishDate | 2025-06-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj-art-7b581504151b473abb738d79b797f96d2025-08-20T03:05:29ZengBMCGenome Biology1474-760X2025-06-0126113210.1186/s13059-025-03615-5Loop Catalog: a comprehensive HiChIP database of human and mouse samplesJoaquin Reyna0Kyra Fetter1Romeo Ignacio2Cemil Can Ali Marandi3Astoria Ma4Nikhil Rao5Zichen Jiang6Daniela Salgado Figueroa7Sourya Bhattacharyya8Ferhat Ay9Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for ImmunologyCenters for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for ImmunologyCenters for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for ImmunologyCenters for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for ImmunologyCenters for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for ImmunologyCenters for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for ImmunologyCenters for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for ImmunologyCenters for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for ImmunologyCenters for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for ImmunologyCenters for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for ImmunologyAbstract HiChIP enables cost-effective and high-resolution profiling of chromatin loops. To leverage the increasing number of HiChIP datasets, we develop Loop Catalog ( https://loopcatalog.lji.org ), a web-based database featuring loop calls from over 1000 distinct human and mouse HiChIP samples from 152 studies plus 44 high-resolution Hi-C samples. We demonstrate its utility for interpreting GWAS and eQTL variants through SNP-to-gene linking, identifying enriched sequence motifs and motif pairs, and generating regulatory networks and 2D representations of chromatin structure. Our catalog spans more than 4.19M unique loops, and with embedded analysis modules, constitutes an important resource for the field.https://doi.org/10.1186/s13059-025-03615-5HiChIPChromatin loopsDatabaseGWASSNP-to-gene linking |
| spellingShingle | Joaquin Reyna Kyra Fetter Romeo Ignacio Cemil Can Ali Marandi Astoria Ma Nikhil Rao Zichen Jiang Daniela Salgado Figueroa Sourya Bhattacharyya Ferhat Ay Loop Catalog: a comprehensive HiChIP database of human and mouse samples Genome Biology HiChIP Chromatin loops Database GWAS SNP-to-gene linking |
| title | Loop Catalog: a comprehensive HiChIP database of human and mouse samples |
| title_full | Loop Catalog: a comprehensive HiChIP database of human and mouse samples |
| title_fullStr | Loop Catalog: a comprehensive HiChIP database of human and mouse samples |
| title_full_unstemmed | Loop Catalog: a comprehensive HiChIP database of human and mouse samples |
| title_short | Loop Catalog: a comprehensive HiChIP database of human and mouse samples |
| title_sort | loop catalog a comprehensive hichip database of human and mouse samples |
| topic | HiChIP Chromatin loops Database GWAS SNP-to-gene linking |
| url | https://doi.org/10.1186/s13059-025-03615-5 |
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