Graph-based Characterisations of Cell Types and Functionally Related Modules in Promoter Capture Hi-C Data

Lelde Lace, Gatis Melkus, Peteris Rucevskis, Edgars Celms, Karlis Cerans, Paulis Kikusts, Mārtiņš Opmanis, Darta Rituma, Juris Viksna

2019

Abstract

Current technologies, noteworthy Hi-C, for chromosome conformation capture allow to understand a broad spectrum of functional interactions between genome elements. Although significant progress has been made, there are still a lot of open questions regarding best approaches for analysis of Hi-C data to identify biologically significant features. In this paper we approach this problem by focusing strictly on the topological properties of Hi-C interaction graphs. Graph topological properties were analysed from the perspective of two research questions: 1) are topological properties alone able to distinguish between different cell types and assign biologically meaningful distances between them; 2) what is a typical structure of Hi-C interaction graphs and can we assign a biological significance to structural elements or features? The analysis was applied to a set of Hi-C interactions in 17 human haematopoietic cell types. Promising results have been obtained at answering both questions. Firstly, we propose a concrete set Base11 of 11 topology-based metrics that provide good discriminatory power between cell types. Secondly, we have explored the topological features of connected components of Hi-C interaction graphs and demonstrate that such components tend to be well conserved within particular cell type subgroups and can be well associated with known biological processes.

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Paper Citation


in Harvard Style

Lace L., Melkus G., Rucevskis P., Celms E., Cerans K., Kikusts P., Opmanis M., Rituma D. and Viksna J. (2019). Graph-based Characterisations of Cell Types and Functionally Related Modules in Promoter Capture Hi-C Data. In Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - Volume 3: BIOINFORMATICS; ISBN 978-989-758-353-7, SciTePress, pages 78-89. DOI: 10.5220/0007390800780089


in Bibtex Style

@conference{bioinformatics19,
author={Lelde Lace and Gatis Melkus and Peteris Rucevskis and Edgars Celms and Karlis Cerans and Paulis Kikusts and Mārtiņš Opmanis and Darta Rituma and Juris Viksna},
title={Graph-based Characterisations of Cell Types and Functionally Related Modules in Promoter Capture Hi-C Data},
booktitle={Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - Volume 3: BIOINFORMATICS},
year={2019},
pages={78-89},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0007390800780089},
isbn={978-989-758-353-7},
}


in EndNote Style

TY - CONF

JO - Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - Volume 3: BIOINFORMATICS
TI - Graph-based Characterisations of Cell Types and Functionally Related Modules in Promoter Capture Hi-C Data
SN - 978-989-758-353-7
AU - Lace L.
AU - Melkus G.
AU - Rucevskis P.
AU - Celms E.
AU - Cerans K.
AU - Kikusts P.
AU - Opmanis M.
AU - Rituma D.
AU - Viksna J.
PY - 2019
SP - 78
EP - 89
DO - 10.5220/0007390800780089
PB - SciTePress