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Among various chromatin conformation capture methods, HiChIP has received increasing attention for its significant improvement over other methods in profiling of regulatory (e.g. H3K27ac) and structural (e.g. cohesin) interactions. To facilitate the studies of 3D regulatory interactions, we developed a HiChIP interactions database, HiChIPdb (http:\/\/health.tsinghua.edu.cn\/hichipdb\/). The current version of HiChIPdb contains \u223c262M annotated HiChIP interactions from 200 high-throughput HiChIP samples across 108 cell types. The functionalities of HiChIPdb include: (i) standardized categorization of HiChIP interactions in a hierarchical structure based on organ, tissue and cell line and (ii) comprehensive annotations of HiChIP interactions with regulatory genes and GWAS Catalog SNPs. To the best of our knowledge, HiChIPdb is the first comprehensive database that utilizes a unified pipeline to map the functional interactions across diverse cell types and tissues in different resolutions. We believe this database has the potential to advance cutting-edge research in regulatory mechanisms in development and disease by removing the barrier in data aggregation, preprocessing, and analysis.<\/jats:p>","DOI":"10.1093\/nar\/gkac859","type":"journal-article","created":{"date-parts":[[2022,10,10]],"date-time":"2022-10-10T20:27:12Z","timestamp":1665433632000},"page":"D159-D166","source":"Crossref","is-referenced-by-count":35,"title":["HiChIPdb: a comprehensive database of HiChIP regulatory interactions"],"prefix":"10.1093","volume":"51","author":[{"given":"Wanwen","family":"Zeng","sequence":"first","affiliation":[{"name":"Department of Statistics, Stanford University , Stanford, CA 94305, USA"},{"name":"Bio-X Program, Stanford University , Stanford, CA 94305, USA"},{"name":"College of Software, Nankai University , Tianjin\u00a0300350, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qiao","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Statistics, Stanford University , Stanford, CA 94305, USA"},{"name":"Bio-X Program, Stanford University , Stanford, CA 94305, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qijin","family":"Yin","sequence":"additional","affiliation":[{"name":"Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University , Beijing 100084, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7533-3753","authenticated-orcid":false,"given":"Rui","family":"Jiang","sequence":"additional","affiliation":[{"name":"Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University , Beijing 100084, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7466-2339","authenticated-orcid":false,"given":"Wing Hung","family":"Wong","sequence":"additional","affiliation":[{"name":"Department of Statistics, Stanford University , Stanford, CA 94305, USA"},{"name":"Department of Biomedical Data Science, Stanford University , Stanford, CA 94305, USA"},{"name":"Bio-X Program, Stanford University , Stanford, CA 94305, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,10,10]]},"reference":[{"key":"2023010804292301300_B1","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1038\/s41576-019-0209-0","article-title":"Towards a comprehensive catalogue of validated and target-linked human enhancers","volume":"21","author":"Gasperini","year":"2020","journal-title":"Nat. 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