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

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.

Download


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 - Volume 3: BIOINFORMATICS, ISBN 978-989-758-353-7, 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 - 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 - 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