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Introducing the novel Cytoscape app TimeNexus to analyze time-series data using temporal MultiLayer Networks (tMLNs)

Authors
  • Pierrelée, Michaël1
  • Reynders, Ana2
  • Lopez, Fabrice3
  • Moqrich, Aziz2
  • Tichit, Laurent4
  • Habermann, Bianca H.1, 5
  • 1 Aix-Marseille University, CNRS, IBDM UMR 7288, Computational Biology Team, Turing Centre for Living Systems (CENTURI), Marseille, France , Marseille (France)
  • 2 Aix-Marseille University, CNRS, IBDM UMR 7288, Team Chronic Pain: Molecular and Cellular Mechanisms, Turing Centre for Living systems (CENTURI), Marseille, France , Marseille (France)
  • 3 Aix-Marseille University, INSERM, TAGC U 1090, Marseille, France , Marseille (France)
  • 4 Aix-Marseille University, CNRS, I2M UMR 7373, Turing Centre for Living Systems (CENTURI), Marseille, France , Marseille (France)
  • 5 Aix-Marseille University, CNRS, IBDM UMR 7288, Turing Center for Living Systems (CENTURI), Parc Scientifique de Luminy, Case 907, 163, Avenue de Luminy, Marseille, 13009, France , Marseille (France)
Type
Published Article
Journal
Scientific Reports
Publisher
Springer Nature
Publication Date
Jul 01, 2021
Volume
11
Issue
1
Identifiers
DOI: 10.1038/s41598-021-93128-5
Source
Springer Nature
Disciplines
  • article
License
Green

Abstract

Integrating -omics data with biological networks such as protein–protein interaction networks is a popular and useful approach to interpret expression changes of genes in changing conditions, and to identify relevant cellular pathways, active subnetworks or network communities. Yet, most -omics data integration tools are restricted to static networks and therefore cannot easily be used for analyzing time-series data. Determining regulations or exploring the network structure over time requires time-dependent networks which incorporate time as one component in their structure. Here, we present a method to project time-series data on sequential layers of a multilayer network, thus creating a temporal multilayer network (tMLN). We implemented this method as a Cytoscape app we named TimeNexus. TimeNexus allows to easily create, manage and visualize temporal multilayer networks starting from a combination of node and edge tables carrying the information on the temporal network structure. To allow further analysis of the tMLN, TimeNexus creates and passes on regular Cytoscape networks in form of static versions of the tMLN in three different ways: (i) over the entire set of layers, (ii) over two consecutive layers at a time, (iii) or on one single layer at a time. We combined TimeNexus with the Cytoscape apps PathLinker and AnatApp/ANAT to extract active subnetworks from tMLNs. To test the usability of our app, we applied TimeNexus together with PathLinker or ANAT on temporal expression data of the yeast cell cycle and were able to identify active subnetworks relevant for different cell cycle phases. We furthermore used TimeNexus on our own temporal expression data from a mouse pain assay inducing hindpaw inflammation and detected active subnetworks relevant for an inflammatory response to injury, including immune response, cell stress response and regulation of apoptosis. TimeNexus is freely available from the Cytoscape app store at https://apps.cytoscape.org/apps/TimeNexus.

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