FIREcaller: Detecting frequently interacting regions from Hi-C data
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Abstract
Hi-C experiments have been widely adopted to study chromatin spatial organization, which plays an essential role in genome function. We have recently identified frequently interacting regions (FIREs) and found that they are closely associated with cell-type-specific gene regulation. However, computational tools for detecting FIREs from Hi-C data are still lacking. In this work, we present FIREcaller, a stand-alone, user-friendly R package for detecting FIREs from Hi-C data. FIREcaller takes raw Hi-C contact matrices as input, performs within-sample and cross-sample normalization, and outputs continuous FIRE scores, dichotomous FIREs, and super-FIREs. Applying FIREcaller to Hi-C data from various human tissues, we demonstrate that FIREs and super-FIREs identified, in a tissue-specific manner, are closely related to gene regulation, are enriched for enhancer-promoter (E-P) interactions, tend to overlap with regions exhibiting epigenomic signatures of cis-regulatory roles, and aid the interpretation or GWAS variants. The FIREcaller package is implemented in R and freely available at https://yunliweb.its.unc.edu/FIREcaller.
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There are 3,966 FIREs in NeuN+ cells and 3,967 FIREs in NeuN− cells.
“We detected 3966 and 3967 FIREs in NeuN+ and NeuN− cells, respectively (Fig. 1a and Supplementary Data 1)24.”
From Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders (2021) · cites this paper as [24]
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Parallel analysis of transcription, integration, and sequence of single HIV-1 proviruses
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- Authors
- Crowley, C., Yang, Y., Qiu, Y., Hu, B., Abnousi, A., Lipiński, J., Plewczyński, D., Wu, D., Won, H., Ren, B., Hu, M., & Li, Y.
- Affiliations
- University of North Carolina at Chapel Hill (US)
- University of California San Diego (US)
- Cleveland Clinic (US)
- Cellular Genomics, Warsaw, Poland
- Warsaw University of Technology (PL)
- Corresponding author
- Yang, Yuchen
- Hu, Ming
- Li, Yun
- ORCID
- Venue
- Computational and Structural Biotechnology Journal
- Published
- 2020-12-31
- Volume
- 19
- Pages
- 355-362
- ISSN
- 2001-0370 (ISSN-L)
- PMC
- PMC7788093
- OpenAlex
- W3117820463
- Cited by
- 37
- References
- 42
- Citations by year
- 2026: 5 · 2025: 4 · 2024: 6 · 2022: 9 · 2021: 13
- FWCI
- 1.95
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Computational and Structural Biotechnology Journal (publishedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- University of North Carolina at Chapel Hill
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- chromatin spatial organization, enhancer-promoter interactions, cell type-specific gene regulation, cis-regulatory elements, R package
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