CytoMCS: A Multiple Maximum Common Subgraph Detection Tool for Cytoscape

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Resumé

Comparative analysis of biological networks is a major problem in computational integrative systems biology. By computing the maximum common edge subgraph between a set of networks, one is able to detect conserved substructures between them and quantify their topological similarity. To aid such analyses we have developed CytoMCS, a Cytoscape app for computing inexact solutions to the maximum common edge subgraph problem for two or more graphs. Our algorithm uses an iterative local search heuristic for computing conserved subgraphs, optimizing a squared edge conservation score that is able to detect not only fully conserved edges but also partially conserved edges. It can be applied to any set of directed or undirected, simple graphs loaded as networks into Cytoscape, e.g. protein-protein interaction networks or gene regulatory networks. CytoMCS is available as a Cytoscape app at http://apps.cytoscape.org/apps/cytomcs.
OriginalsprogEngelsk
Artikelnummer20170014
TidsskriftJournal of Integrative Bioinformatics
Vol/bind14
Udgave nummer2
Antal sider8
ISSN1613-4516
DOI
StatusUdgivet - 21. jul. 2017
Begivenhed13th Annual Meeting of the International Symposium on Integrative Bioinformatics - University of Southern Denmark, Campusvej 55 5230 Odense, Odense, Danmark
Varighed: 22. jun. 201724. jun. 2017
Konferencens nummer: 13
http://www.imbio.de/ib2017/program.php

Konference

Konference13th Annual Meeting of the International Symposium on Integrative Bioinformatics
Nummer13
LokationUniversity of Southern Denmark, Campusvej 55 5230 Odense
LandDanmark
ByOdense
Periode22/06/201724/06/2017
Internetadresse

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title = "CytoMCS: A Multiple Maximum Common Subgraph Detection Tool for Cytoscape",
abstract = "Comparative analysis of biological networks is a major problem in computational integrative systems biology. By computing the maximum common edge subgraph between a set of networks, one is able to detect conserved substructures between them and quantify their topological similarity. To aid such analyses we have developed CytoMCS, a Cytoscape app for computing inexact solutions to the maximum common edge subgraph problem for two or more graphs. Our algorithm uses an iterative local search heuristic for computing conserved subgraphs, optimizing a squared edge conservation score that is able to detect not only fully conserved edges but also partially conserved edges. It can be applied to any set of directed or undirected, simple graphs loaded as networks into Cytoscape, e.g. protein-protein interaction networks or gene regulatory networks. CytoMCS is available as a Cytoscape app at http://apps.cytoscape.org/apps/cytomcs.",
keywords = "global network alignment, local search, network alignment, networks, Heuristics, Humans, Arabidopsis/genetics, Gene Regulatory Networks, Saccharomyces cerevisiae/genetics, Protein Interaction Maps, Algorithms, Animals, Mice, Software, Systems Biology/methods",
author = "Simon Larsen and Jan Baumbach",
year = "2017",
month = "7",
day = "21",
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language = "English",
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journal = "Journal of Integrative Bioinformatics",
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}

CytoMCS: A Multiple Maximum Common Subgraph Detection Tool for Cytoscape. / Larsen, Simon; Baumbach, Jan.

I: Journal of Integrative Bioinformatics, Bind 14, Nr. 2, 20170014, 21.07.2017.

Publikation: Bidrag til tidsskriftKonferenceartikelForskningpeer review

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AB - Comparative analysis of biological networks is a major problem in computational integrative systems biology. By computing the maximum common edge subgraph between a set of networks, one is able to detect conserved substructures between them and quantify their topological similarity. To aid such analyses we have developed CytoMCS, a Cytoscape app for computing inexact solutions to the maximum common edge subgraph problem for two or more graphs. Our algorithm uses an iterative local search heuristic for computing conserved subgraphs, optimizing a squared edge conservation score that is able to detect not only fully conserved edges but also partially conserved edges. It can be applied to any set of directed or undirected, simple graphs loaded as networks into Cytoscape, e.g. protein-protein interaction networks or gene regulatory networks. CytoMCS is available as a Cytoscape app at http://apps.cytoscape.org/apps/cytomcs.

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KW - Heuristics

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KW - Protein Interaction Maps

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KW - Mice

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