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An Augmented High-Dimensional Graphical Lasso Method to Incorporate Prior Biological Knowledge for Global Network Learning

Biological networks are often inferred through Gaussian graphical models (GGMs) using gene or protein expression data only. GGMs identify conditional dependence by estimating a precision matrix between genes or proteins. However, conventional GGM approaches often ignore prior knowledge about protein...

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Autores principales: Zhuang, Yonghua, Xing, Fuyong, Ghosh, Debashis, Banaei-Kashani, Farnoush, Bowler, Russell P., Kechris, Katerina
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8829118/
https://www.ncbi.nlm.nih.gov/pubmed/35154240
http://dx.doi.org/10.3389/fgene.2021.760299
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author Zhuang, Yonghua
Xing, Fuyong
Ghosh, Debashis
Banaei-Kashani, Farnoush
Bowler, Russell P.
Kechris, Katerina
author_facet Zhuang, Yonghua
Xing, Fuyong
Ghosh, Debashis
Banaei-Kashani, Farnoush
Bowler, Russell P.
Kechris, Katerina
author_sort Zhuang, Yonghua
collection PubMed
description Biological networks are often inferred through Gaussian graphical models (GGMs) using gene or protein expression data only. GGMs identify conditional dependence by estimating a precision matrix between genes or proteins. However, conventional GGM approaches often ignore prior knowledge about protein-protein interactions (PPI). Recently, several groups have extended GGM to weighted graphical Lasso (wGlasso) and network-based gene set analysis (Netgsa) and have demonstrated the advantages of incorporating PPI information. However, these methods are either computationally intractable for large-scale data, or disregard weights in the PPI networks. To address these shortcomings, we extended the Netgsa approach and developed an augmented high-dimensional graphical Lasso (AhGlasso) method to incorporate edge weights in known PPI with omics data for global network learning. This new method outperforms weighted graphical Lasso-based algorithms with respect to computational time in simulated large-scale data settings while achieving better or comparable prediction accuracy of node connections. The total runtime of AhGlasso is approximately five times faster than weighted Glasso methods when the graph size ranges from 1,000 to 3,000 with a fixed sample size (n = 300). The runtime difference between AhGlasso and weighted Glasso increases when the graph size increases. Using proteomic data from a study on chronic obstructive pulmonary disease, we demonstrate that AhGlasso improves protein network inference compared to the Netgsa approach by incorporating PPI information.
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spelling pubmed-88291182022-02-11 An Augmented High-Dimensional Graphical Lasso Method to Incorporate Prior Biological Knowledge for Global Network Learning Zhuang, Yonghua Xing, Fuyong Ghosh, Debashis Banaei-Kashani, Farnoush Bowler, Russell P. Kechris, Katerina Front Genet Genetics Biological networks are often inferred through Gaussian graphical models (GGMs) using gene or protein expression data only. GGMs identify conditional dependence by estimating a precision matrix between genes or proteins. However, conventional GGM approaches often ignore prior knowledge about protein-protein interactions (PPI). Recently, several groups have extended GGM to weighted graphical Lasso (wGlasso) and network-based gene set analysis (Netgsa) and have demonstrated the advantages of incorporating PPI information. However, these methods are either computationally intractable for large-scale data, or disregard weights in the PPI networks. To address these shortcomings, we extended the Netgsa approach and developed an augmented high-dimensional graphical Lasso (AhGlasso) method to incorporate edge weights in known PPI with omics data for global network learning. This new method outperforms weighted graphical Lasso-based algorithms with respect to computational time in simulated large-scale data settings while achieving better or comparable prediction accuracy of node connections. The total runtime of AhGlasso is approximately five times faster than weighted Glasso methods when the graph size ranges from 1,000 to 3,000 with a fixed sample size (n = 300). The runtime difference between AhGlasso and weighted Glasso increases when the graph size increases. Using proteomic data from a study on chronic obstructive pulmonary disease, we demonstrate that AhGlasso improves protein network inference compared to the Netgsa approach by incorporating PPI information. Frontiers Media S.A. 2022-01-27 /pmc/articles/PMC8829118/ /pubmed/35154240 http://dx.doi.org/10.3389/fgene.2021.760299 Text en Copyright © 2022 Zhuang, Xing, Ghosh, Banaei-Kashani, Bowler and Kechris. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Zhuang, Yonghua
Xing, Fuyong
Ghosh, Debashis
Banaei-Kashani, Farnoush
Bowler, Russell P.
Kechris, Katerina
An Augmented High-Dimensional Graphical Lasso Method to Incorporate Prior Biological Knowledge for Global Network Learning
title An Augmented High-Dimensional Graphical Lasso Method to Incorporate Prior Biological Knowledge for Global Network Learning
title_full An Augmented High-Dimensional Graphical Lasso Method to Incorporate Prior Biological Knowledge for Global Network Learning
title_fullStr An Augmented High-Dimensional Graphical Lasso Method to Incorporate Prior Biological Knowledge for Global Network Learning
title_full_unstemmed An Augmented High-Dimensional Graphical Lasso Method to Incorporate Prior Biological Knowledge for Global Network Learning
title_short An Augmented High-Dimensional Graphical Lasso Method to Incorporate Prior Biological Knowledge for Global Network Learning
title_sort augmented high-dimensional graphical lasso method to incorporate prior biological knowledge for global network learning
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8829118/
https://www.ncbi.nlm.nih.gov/pubmed/35154240
http://dx.doi.org/10.3389/fgene.2021.760299
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