HiCMC

High-Efficiency Contact Matrix Compressor

authored by

Yeremia Gunawan Adhisantoso, Tim Körner, Fabian Müntefering, Jörn Ostermann, Jan Voges

Abstract

Background: Chromosome organization plays an important role in biological processes such as replication, regulation, and transcription. One way to study the relationship between chromosome structure and its biological functions is through Hi-C studies, a genome-wide method for capturing chromosome conformation. Such studies generate vast amounts of data. The problem is exacerbated by the fact that chromosome organization is dynamic, requiring snapshots at different points in time, further increasing the amount of data to be stored. We present a novel approach called the High-Efficiency Contact Matrix Compressor (HiCMC) for efficient compression of Hi-C data. Results: By modeling the underlying structures found in the contact matrix, such as compartments and domains, HiCMC outperforms the state-of-the-art method CMC by approximately 8% and the other state-of-the-art methods cooler, LZMA, and bzip2 by over 50% across multiple cell lines and contact matrix resolutions. In addition, HiCMC integrates domain-specific information into the compressed bitstreams that it generates, and this information can be used to speed up downstream analyses. Conclusion: HiCMC is a novel compression approach that utilizes intrinsic properties of contact matrix, such as compartments and domains. It allows for a better compression in comparison to the state-of-the-art methods. HiCMC is available at github.com/sXperfect/hicmc.

Organisation(s)

Institute of Information Processing
L3S Research Centre

External Organisation(s)

University of Navarra
IdiSNA

Type

Article

Journal

BMC BIOINFORMATICS

Volume

No. of pages

ISSN

1471-2105

Publication date

2024

Publication status

Published

Peer reviewed

Yes

ASJC Scopus subject areas

Structural Biology, Biochemistry, Molecular Biology, Computer Science Applications, Applied Mathematics

Electronic version(s)

https://doi.org/10.1186/s12859-024-05907-2 (Access: Open)

BibTeX

@article{c7a8285d132443d0add8848dc4cf9d00,
title = "HiCMC: High-Efficiency Contact Matrix Compressor",
abstract = "Background: Chromosome organization plays an important role in biological processes such as replication, regulation, and transcription. One way to study the relationship between chromosome structure and its biological functions is through Hi-C studies, a genome-wide method for capturing chromosome conformation. Such studies generate vast amounts of data. The problem is exacerbated by the fact that chromosome organization is dynamic, requiring snapshots at different points in time, further increasing the amount of data to be stored. We present a novel approach called the High-Efficiency Contact Matrix Compressor (HiCMC) for efficient compression of Hi-C data. Results: By modeling the underlying structures found in the contact matrix, such as compartments and domains, HiCMC outperforms the state-of-the-art method CMC by approximately 8% and the other state-of-the-art methods cooler, LZMA, and bzip2 by over 50% across multiple cell lines and contact matrix resolutions. In addition, HiCMC integrates domain-specific information into the compressed bitstreams that it generates, and this information can be used to speed up downstream analyses. Conclusion: HiCMC is a novel compression approach that utilizes intrinsic properties of contact matrix, such as compartments and domains. It allows for a better compression in comparison to the state-of-the-art methods. HiCMC is available at https://github.com/sXperfect/hicmc.",
keywords = "3C, Compression, Contact matrix, Hi-C",
author = "Adhisantoso, {Yeremia Gunawan} and Tim K{\"o}rner and Fabian M{\"u}ntefering and J{\"o}rn Ostermann and Jan Voges",
note = "Publisher Copyright: {\textcopyright} The Author(s) 2024.",
year = "2024",
doi = "10.1186/s12859-024-05907-2",
language = "English",
volume = "25",
journal = "BMC BIOINFORMATICS",
issn = "1471-2105",
publisher = "BioMed Central Ltd.",
number = "1",
}