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NetSHy: network summarization via a hybrid approach leveraging topological properties

MOTIVATION: Biological networks can provide a system-level understanding of underlying processes. In many contexts, networks have a high degree of modularity, i.e. they consist of subsets of nodes, often known as subnetworks or modules, which are highly interconnected and may perform separate functi...

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Autores principales: Vu, Thao, Litkowski, Elizabeth M, Liu, Weixuan, Pratte, Katherine A, Lange, Leslie, Bowler, Russell P, Banaei-Kashani, Farnoush, Kechris, Katerina J
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9831052/
https://www.ncbi.nlm.nih.gov/pubmed/36548341
http://dx.doi.org/10.1093/bioinformatics/btac818
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author Vu, Thao
Litkowski, Elizabeth M
Liu, Weixuan
Pratte, Katherine A
Lange, Leslie
Bowler, Russell P
Banaei-Kashani, Farnoush
Kechris, Katerina J
author_facet Vu, Thao
Litkowski, Elizabeth M
Liu, Weixuan
Pratte, Katherine A
Lange, Leslie
Bowler, Russell P
Banaei-Kashani, Farnoush
Kechris, Katerina J
author_sort Vu, Thao
collection PubMed
description MOTIVATION: Biological networks can provide a system-level understanding of underlying processes. In many contexts, networks have a high degree of modularity, i.e. they consist of subsets of nodes, often known as subnetworks or modules, which are highly interconnected and may perform separate functions. In order to perform subsequent analyses to investigate the association between the identified module and a variable of interest, a module summarization, that best explains the module’s information and reduces dimensionality is often needed. Conventional approaches for obtaining network representation typically rely only on the profiles of the nodes within the network while disregarding the inherent network topological information. RESULTS: In this article, we propose NetSHy, a hybrid approach which is capable of reducing the dimension of a network while incorporating topological properties to aid the interpretation of the downstream analyses. In particular, NetSHy applies principal component analysis (PCA) on a combination of the node profiles and the well-known Laplacian matrix derived directly from the network similarity matrix to extract a summarization at a subject level. Simulation scenarios based on random and empirical networks at varying network sizes and sparsity levels show that NetSHy outperforms the conventional PCA approach applied directly on node profiles, in terms of recovering the true correlation with a phenotype of interest and maintaining a higher amount of explained variation in the data when networks are relatively sparse. The robustness of NetSHy is also demonstrated by a more consistent correlation with the observed phenotype as the sample size decreases. Lastly, a genome-wide association study is performed as an application of a downstream analysis, where NetSHy summarization scores on the biological networks identify more significant single nucleotide polymorphisms than the conventional network representation. AVAILABILITY AND IMPLEMENTATION: R code implementation of NetSHy is available at https://github.com/thaovu1/NetSHy SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-98310522023-01-10 NetSHy: network summarization via a hybrid approach leveraging topological properties Vu, Thao Litkowski, Elizabeth M Liu, Weixuan Pratte, Katherine A Lange, Leslie Bowler, Russell P Banaei-Kashani, Farnoush Kechris, Katerina J Bioinformatics Original Paper MOTIVATION: Biological networks can provide a system-level understanding of underlying processes. In many contexts, networks have a high degree of modularity, i.e. they consist of subsets of nodes, often known as subnetworks or modules, which are highly interconnected and may perform separate functions. In order to perform subsequent analyses to investigate the association between the identified module and a variable of interest, a module summarization, that best explains the module’s information and reduces dimensionality is often needed. Conventional approaches for obtaining network representation typically rely only on the profiles of the nodes within the network while disregarding the inherent network topological information. RESULTS: In this article, we propose NetSHy, a hybrid approach which is capable of reducing the dimension of a network while incorporating topological properties to aid the interpretation of the downstream analyses. In particular, NetSHy applies principal component analysis (PCA) on a combination of the node profiles and the well-known Laplacian matrix derived directly from the network similarity matrix to extract a summarization at a subject level. Simulation scenarios based on random and empirical networks at varying network sizes and sparsity levels show that NetSHy outperforms the conventional PCA approach applied directly on node profiles, in terms of recovering the true correlation with a phenotype of interest and maintaining a higher amount of explained variation in the data when networks are relatively sparse. The robustness of NetSHy is also demonstrated by a more consistent correlation with the observed phenotype as the sample size decreases. Lastly, a genome-wide association study is performed as an application of a downstream analysis, where NetSHy summarization scores on the biological networks identify more significant single nucleotide polymorphisms than the conventional network representation. AVAILABILITY AND IMPLEMENTATION: R code implementation of NetSHy is available at https://github.com/thaovu1/NetSHy SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2022-12-22 /pmc/articles/PMC9831052/ /pubmed/36548341 http://dx.doi.org/10.1093/bioinformatics/btac818 Text en © The Author(s) 2022. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Paper
Vu, Thao
Litkowski, Elizabeth M
Liu, Weixuan
Pratte, Katherine A
Lange, Leslie
Bowler, Russell P
Banaei-Kashani, Farnoush
Kechris, Katerina J
NetSHy: network summarization via a hybrid approach leveraging topological properties
title NetSHy: network summarization via a hybrid approach leveraging topological properties
title_full NetSHy: network summarization via a hybrid approach leveraging topological properties
title_fullStr NetSHy: network summarization via a hybrid approach leveraging topological properties
title_full_unstemmed NetSHy: network summarization via a hybrid approach leveraging topological properties
title_short NetSHy: network summarization via a hybrid approach leveraging topological properties
title_sort netshy: network summarization via a hybrid approach leveraging topological properties
topic Original Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9831052/
https://www.ncbi.nlm.nih.gov/pubmed/36548341
http://dx.doi.org/10.1093/bioinformatics/btac818
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