Document Type

Article

Publication Date

2023

DOI

10.1093/bioinformatics/btad211

Publication Title

Bioinformatics

Volume

39

Issue

5

Pages

btad211 (1-8)

Abstract

Motivation: Hi-C technology has been the most widely used chromosome conformation capture(3C) experiment that measures the frequency of all paired interactions in the entire genome, which is a powerful tool for studying the 3D structure of the genome. The fineness of the constructed genome structure depends on the resolution of Hi-C data. However, due to the fact that high-resolution Hi-C data require deep sequencing and thus high experimental cost, most available Hi-C data are in low-resolution. Hence, it is essential to enhance the quality of Hi-C data by developing the effective computational methods.

Results: In this work, we propose a novel method, so-called DFHiC, which generates the high-resolution Hi-C matrix from the low-resolution Hi-C matrix in the framework of the dilated convolutional neural network. The dilated convolution is able to effectively explore the global patterns in the overall Hi-C matrix by taking advantage of the information of the Hi-C matrix in a way of the longer genomic distance. Consequently, DFHiC can improve the resolution of the Hi-C matrix reliably and accurately. More importantly, the super-resolution Hi-C data enhanced by DFHiC is more in line with the real high-resolution Hi-C data than those done by the other existing methods, in terms of both chromatin significant interactions and identifying topologically associating domains (TADs).

Availability and implementation: https://github.com/BinWangCSU/DFHiC.

Rights

© The Authors 2023.

This is an Open Access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Data Availability

Article states: Supplementary data are available at Bioinformatics online.

Original Publication Citation

Wang, B., Liu, K., Li, Y., & Wang, J. (2023). DFHiC: A dilated full convolution model to enhance the resolution of Hi-C data. Bioinformatics, 39(5), 1-8, Article btad211. https://doi.org/10.1093/bioinformatics/btad211

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