PreprintCited by 577Genomics and Chromatin DynamicsGenomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalities

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HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

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Yang, Tao, Zhang, Feipeng, Yardımcı, Galip Gürkan, Song, Fan, Hardison, Ross C., Noble, William Stafford, Yue, Feng, Li, Qunhua·2017·Genome Research

DOI 10.1101/gr.220640.117PMC PMC5668950

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Abstract

Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce misleading results because they ignore spatial features in Hi-C data, such as domain structure and distance dependence. We present HiCRep, a framework for assessing the reproducibility of Hi-C data that systematically accounts for these features. In particular, we introduce a novel similarity measure, the stratum adjusted correlation coefficient (SCC), for quantifying the similarity between Hi-C interaction matrices. Not only does it provide a statistically sound and reliable evaluation of reproducibility, SCC can also be used to quantify differences between Hi-C contact matrices and to determine the optimal sequencing depth for a desired resolution. The measure consistently shows higher accuracy than existing approaches in distinguishing subtle differences in reproducibility and depicting interrelationships of cell lineages. The proposed measure is straightforward to interpret and easy to compute, making it well-suited for providing standardized, interpretable, automatable, and scalable quality control. The freely available R package HiCRep implements our approach.

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Additional file 4 of Mapping DNA interaction landscapes in psoriasis susceptibility loci highlights KLF4 as a target gene in 9q31
Ray-Jones, H. F., Duffus, K., McGovern, A., Martin, P., Shi, C., Hankinson, J., Gough, O., Yarwood, A., Morris, A. P., Adamson, A. D., et al. (2020) · Figshare · doi:10.6084/m9.figshare.12246902
Additional file 11 of Improved quality metrics for association and reproducibility in chromatin accessibility data using mutual information
Roth, C., Venu, V., Job, V., Lubbers, N., Sanbonmatsu, K. Y., Steadman, C. R., & Starkenburg, S. R. (2024) · Figshare · doi:10.6084/m9.figshare.26643586
Additional file 4 of Cellular reprogramming is driven by widespread rewiring of promoter-enhancer interactions
Wang, M., He, B., Hao, Y., Srinivasan, D., Shrinet, J., & Fraser, P. (2024) · Figshare · doi:10.6084/m9.figshare.26642452
Additional file 2 of Cellular reprogramming is driven by widespread rewiring of promoter-enhancer interactions
Wang, M., He, B., Hao, Y., Srinivasan, D., Shrinet, J., & Fraser, P. (2024) · Figshare · doi:10.6084/m9.figshare.26642443
Additional file 7 of High-resolution Hi-C maps highlight multiscale 3D epigenome reprogramming during pancreatic cancer metastasis
Ren, B., Yang, J., Wang, C., Yang, G., Wang, H., Chen, Y., Xu, R., Fan, X., You, L., Zhang, T., et al. (2021) · Figshare · doi:10.6084/m9.figshare.15110094
Additional file 2 of Comparative 3D genome architecture in vertebrates
Li, D., He, M., Tang, Q., Tian, S., Zhang, J., Li, Y., Wang, D., Jin, L., Ning, C., Zhu, W., et al. (2022) · Figshare · doi:10.6084/m9.figshare.19728046
Additional file 2 of Multiple epigenetic factors co-localize with HMGN proteins in A-compartment chromatin
He, B., Zhu, I., Postnikov, Y. V., Furusawa, T., Jenkins, L., Nanduri, R., Bustin, M., & Landsman, D. (2022) · Figshare · doi:10.6084/m9.figshare.20166942
Additional file 24 of Exploring the dynamic three-dimensional chromatin architecture and transcriptional landscape in goose liver tissues underlying metabolic adaptations induced by a high-fat diet
Gao, G., Liu, R., Hu, S., He, M., Zhang, J., Gao, D., Li, J., Hu, J., Wang, J., Wang, Q., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26699096
Additional file 4 of Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation
Hyle, J. W., Djekidel, M. N., Williams, J., Wright, S., Shao, Y., Xu, B., & Li, C. (2024) · Figshare · doi:10.6084/m9.figshare.26562736
Additional file 6 of Improved quality metrics for association and reproducibility in chromatin accessibility data using mutual information
Roth, C., Venu, V., Job, V., Lubbers, N., Sanbonmatsu, K. Y., Steadman, C. R., & Starkenburg, S. R. (2024) · Figshare · doi:10.6084/m9.figshare.26643571
Additional file 10 of Improved quality metrics for association and reproducibility in chromatin accessibility data using mutual information
Roth, C., Venu, V., Job, V., Lubbers, N., Sanbonmatsu, K. Y., Steadman, C. R., & Starkenburg, S. R. (2024) · Figshare · doi:10.6084/m9.figshare.26643583
Additional file 3 of Exploring the dynamic three-dimensional chromatin architecture and transcriptional landscape in goose liver tissues underlying metabolic adaptations induced by a high-fat diet
Gao, G., Liu, R., Hu, S., He, M., Zhang, J., Gao, D., Li, J., Hu, J., Wang, J., Wang, Q., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26699033
Additional file 16 of Exploring the dynamic three-dimensional chromatin architecture and transcriptional landscape in goose liver tissues underlying metabolic adaptations induced by a high-fat diet
Gao, G., Liu, R., Hu, S., He, M., Zhang, J., Gao, D., Li, J., Hu, J., Wang, J., Wang, Q., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26699072
Additional file 2 of ChIPr: accurate prediction of cohesin-mediated 3D genome organization from 2D chromatin features
Abbas, A. A., Chandratre, K. R., Gao, Y., Yuan, J., Zhang, M. Q., & Mani, R. S. (2024) · Figshare · doi:10.6084/m9.figshare.24993803
Additional file 3 of Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation
Hyle, J. W., Djekidel, M. N., Williams, J., Wright, S., Shao, Y., Xu, B., & Li, C. (2024) · Figshare · doi:10.6084/m9.figshare.26562733
Additional file 8 of Mapping DNA interaction landscapes in psoriasis susceptibility loci highlights KLF4 as a target gene in 9q31
Ray-Jones, H. F., Duffus, K., McGovern, A., Martin, P., Shi, C., Hankinson, J., Gough, O., Yarwood, A., Morris, A. P., Adamson, A. D., et al. (2020) · Figshare · doi:10.6084/m9.figshare.12246926
Additional file 5 of Exploring the dynamic three-dimensional chromatin architecture and transcriptional landscape in goose liver tissues underlying metabolic adaptations induced by a high-fat diet
Gao, G., Liu, R., Hu, S., He, M., Zhang, J., Gao, D., Li, J., Hu, J., Wang, J., Wang, Q., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26699039
Additional file 5 of Functional genomics atlas of synovial fibroblasts defining rheumatoid arthritis heritability
Ge, X. J., Frank‐Bertoncelj, M., Klein, K., McGovern, A., Kuret, T., Houtman, M., Burja, B., Micheroli, R., Shi, C., Marks, M., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16442123
Additional file 14 of Mapping DNA interaction landscapes in psoriasis susceptibility loci highlights KLF4 as a target gene in 9q31
Ray-Jones, H. F., Duffus, K., McGovern, A., Martin, P., Shi, C., Hankinson, J., Gough, O., Yarwood, A., Morris, A. P., Adamson, A. D., et al. (2020) · Figshare · doi:10.6084/m9.figshare.12246872
Additional file 15 of Exploring the dynamic three-dimensional chromatin architecture and transcriptional landscape in goose liver tissues underlying metabolic adaptations induced by a high-fat diet
Gao, G., Liu, R., Hu, S., He, M., Zhang, J., Gao, D., Li, J., Hu, J., Wang, J., Wang, Q., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26699069
Additional file 2 of GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization
Lee, D.-I., & Roy, S. (2021) · Figshare · doi:10.6084/m9.figshare.14676791
Additional file 3 of Reorganization of 3D genome architecture across wild boar and Bama pig adipose tissues
Zhang, J., Liu, P., He, M., Wang, Y., Kui, H., Jin, L., Li, D., & Li, M. (2022) · Figshare · doi:10.6084/m9.figshare.19350068
Additional file 7 of Exploring the dynamic three-dimensional chromatin architecture and transcriptional landscape in goose liver tissues underlying metabolic adaptations induced by a high-fat diet
Gao, G., Liu, R., Hu, S., He, M., Zhang, J., Gao, D., Li, J., Hu, J., Wang, J., Wang, Q., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26699045
Additional file 2 of Exploring the dynamic three-dimensional chromatin architecture and transcriptional landscape in goose liver tissues underlying metabolic adaptations induced by a high-fat diet
Gao, G., Liu, R., Hu, S., He, M., Zhang, J., Gao, D., Li, J., Hu, J., Wang, J., Wang, Q., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26699030
Additional file 22 of Exploring the dynamic three-dimensional chromatin architecture and transcriptional landscape in goose liver tissues underlying metabolic adaptations induced by a high-fat diet
Gao, G., Liu, R., Hu, S., He, M., Zhang, J., Gao, D., Li, J., Hu, J., Wang, J., Wang, Q., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26699090
Additional file 25 of Exploring the dynamic three-dimensional chromatin architecture and transcriptional landscape in goose liver tissues underlying metabolic adaptations induced by a high-fat diet
Gao, G., Liu, R., Hu, S., He, M., Zhang, J., Gao, D., Li, J., Hu, J., Wang, J., Wang, Q., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26699099
Additional file 8 of Exploring the dynamic three-dimensional chromatin architecture and transcriptional landscape in goose liver tissues underlying metabolic adaptations induced by a high-fat diet
Gao, G., Liu, R., Hu, S., He, M., Zhang, J., Gao, D., Li, J., Hu, J., Wang, J., Wang, Q., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26699048
Additional file 8 of Improved quality metrics for association and reproducibility in chromatin accessibility data using mutual information
Roth, C., Venu, V., Job, V., Lubbers, N., Sanbonmatsu, K. Y., Steadman, C. R., & Starkenburg, S. R. (2024) · Figshare · doi:10.6084/m9.figshare.26643577
Additional file 1 of Cellular reprogramming is driven by widespread rewiring of promoter-enhancer interactions
Wang, M., He, B., Hao, Y., Srinivasan, D., Shrinet, J., & Fraser, P. (2024) · Figshare · doi:10.6084/m9.figshare.26642440
Additional file 2 of Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation
Hyle, J. W., Djekidel, M. N., Williams, J., Wright, S., Shao, Y., Xu, B., & Li, C. (2024) · Figshare · doi:10.6084/m9.figshare.26562730
Additional file 5 of Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation
Hyle, J. W., Djekidel, M. N., Williams, J., Wright, S., Shao, Y., Xu, B., & Li, C. (2024) · Figshare · doi:10.6084/m9.figshare.26562739
Additional file 6 of Mapping DNA interaction landscapes in psoriasis susceptibility loci highlights KLF4 as a target gene in 9q31
Ray-Jones, H. F., Duffus, K., McGovern, A., Martin, P., Shi, C., Hankinson, J., Gough, O., Yarwood, A., Morris, A. P., Adamson, A. D., et al. (2020) · Figshare · doi:10.6084/m9.figshare.12246908

Authors: Yang, T., Zhang, F., Yardımcı, G. G., Song, F., Hardison, R. C., Noble, W. S., Yue, F., & Li, Q.
Affiliations: Pennsylvania State University (US)
University of Washington (US)
ORCID: Yang, Tao
Zhang, Feipeng
Yardımcı, Galip Gürkan
Hardison, Ross C.
Noble, William Stafford
Yue, Feng
Li, Qunhua
Venue: Genome Research
Publisher: Cold Spring Harbor Laboratory
Published: 2017-08-30
Volume: 27
Issue: 11
Pages: 1939-1949
ISSN: 1088-9051 (ISSN-L)
1549-5469
DOI: 10.1101/gr.220640.117
PMC: PMC5668950
OpenAlex: W2952940726
Cited by: 533
References: 41
Citations by year: 2026: 48 · 2025: 68 · 2024: 98 · 2023: 69 · 2022: 57 · 2021: 73 · 2020: 60 · 2019: 38 · 2018: 18 · 2017: 4
Type: posted content
Language: en
Open access: hybrid
doi.org
Licence: public-domain
Locations: Genome Research (publishedVersion, public-domain)
bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
PubMed Central (publishedVersion, cc-by-nc)
PubMed (publishedVersion)
HighWire Press Open Archive (submittedVersion)
Funders: National Institutes of Health (T32 GM102057)
Huck Graduate Research Innovation
NIH (R01GM109453, U01CA200060, R24DK106766, U54HG006998, U41HG007000)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
Keywords: Hi-C, domain structure, distance dependence, cell lineage
MeSH terms: Cell Line, Humans, Software, Reproducibility of Results, Sequence Analysis, RNA, Cell Lineage, Computational Biology, Chromatin Immunoprecipitation, High-Throughput Nucleotide Sequencing

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HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

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