Multilayer networks: aspects, implementations, and application in biomedicine

Abstract

Modeling and analyses of complex systems using network theory have been an object of study for a long time. They have caught attention in many disciplines such as sociology, epidemiology, ecology, psychology, biology, biomedicine, and other fields. Network theory is especially an efficient tool to model biological networks such as gene co-expression networks, protein-protein interaction networks, or pathways. Considering the enhanced resolutions of complex real-world systems, the interest has been directed to multilayered networks. However, despite this surge of recent attention, the use of the multilayer framework in the biological field is still in its youth. In this paper, we review the different aspects and terminologies of multilayered networks. We also briefly discuss the variant applications of the multilayer framework, and finally, we give an overview of various existing applications of the multilayer model in network biology.

Comparative Analyses of Gene Co-expression Networks: Implementations and Applications in the Study of Evolution

“…Multilayer networks can provide better modeling for complex networks like biological networks. However, their usage is still new in some domains, including GCNs, but commonly applied in other research areas such as epidemiology (Hammoud and Kramer, 2020). These networks are node-aligned networks with layers representing co-expression profiles in different settings, including different time points, diseases, cells, or organisms (Rai et al, 2017).…”

Network Biology Approaches to Achieve Precision Medicine in Inflammatory Bowel Disease

“…This multi-omics revolution necessitates the combination of various network modelling approaches. Multi-layered networks can be used to integrate the many facets of multi-omics data including the different time scales of biological processes ( Hammoud and Kramer, 2020 ). In recent years, various databases have been developed such as OmniPath ( Türei et al, 2021 ), SignaLink2 ( Fazekas et al, 2013 ), TranscriptomeBrowser ( Lepoivre et al, 2012 ) or ConsensusPathDB ( Kamburov et al, 2011 ), that can be used to generate multi-layered networks to integrate multi-omics data ( Santra et al, 2014 ).…”

Network-Based Approaches Reveal Potential Therapeutic Targets for Host-Directed Antileishmanial Therapy Driving Drug Repurposing

“…However, biological networks represent not only regulatory interactions but also interactions connected by different means, such as nondirected protein-protein interactions or directed metabolic reactions. These aspects are employed in many fields of biomedicine by combining different networks, such as protein-protein interactions (PPIs), GRNs, and epidemiology information ( 24 ). The integration of the information available in the multitude of networks that one can obtain from a biological system is a complex task.…”

“…The integration of the information available in the multitude of networks that one can obtain from a biological system is a complex task. To facilitate this process, multilayered graphs emerge as a solution recently introduced in the field of biomedicine ( 24 ). This concept consists of layering the components of the network, nodes, or edges, grouping them by their type based on the heterogeneity of the network nodes or the relations among them.…”