ModuLand plug-in for Cytoscape: Determination of hierarchical layers of overlapping network modules and community centrality

Máté Szalay-Beko; Robin Palotai; Balázs Szappanos; István A. Kovács; Balázs Papp; Péter Csermely

doi:10.1093/bioinformatics/bts352

ModuLand plug-in for Cytoscape: Determination of hierarchical layers of overlapping network modules and community centrality

Máté Szalay-Beko, Robin Palotai, Balázs Szappanos, István A. Kovács, Balázs Papp, Péter Csermely^*

^*Corresponding author for this work

Physics and Astronomy

Research output: Contribution to journal › Article › peer-review

92 Scopus citations

Abstract

Summary: The ModuLand plug-in provides Cytoscape users an algorithm for determining extensively overlapping network modules. Moreover, it identifies several hierarchical layers of modules, where meta-nodes of the higher hierarchical layer represent modules of the lower layer. The tool assigns module cores, which predict the function of the whole module, and determines key nodes bridging two or multiple modules. The plug-in has a detailed JAVA-based graphical interface with various colouring options. The ModuLand tool can run on Windows, Linux or Mac OS. We demonstrate its use on protein structure and metabolic networks.

Original language	English (US)
Article number	bts352
Pages (from-to)	2202-2204
Number of pages	3
Journal	Bioinformatics
Volume	28
Issue number	16
DOIs	https://doi.org/10.1093/bioinformatics/bts352
State	Published - Aug 2012

Funding

Funding: EU [FP6-518230, TÁMOP-4.2.2/B-10/1-2010-0013 and FP7-264780]; Hungarian Scientific Research Fund [OTKA K-83314 and PD-75261]; International Human Frontiers Science Program Organization (BP); Momentum Program of the Hungarian Academy of Sciences (BP); and residence at the Rockefeller Foundation Bellagio Center (PC).

ASJC Scopus subject areas

Computational Mathematics
Molecular Biology
Biochemistry
Statistics and Probability
Computer Science Applications
Computational Theory and Mathematics

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10.1093/bioinformatics/bts352

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title = "ModuLand plug-in for Cytoscape: Determination of hierarchical layers of overlapping network modules and community centrality",

abstract = "Summary: The ModuLand plug-in provides Cytoscape users an algorithm for determining extensively overlapping network modules. Moreover, it identifies several hierarchical layers of modules, where meta-nodes of the higher hierarchical layer represent modules of the lower layer. The tool assigns module cores, which predict the function of the whole module, and determines key nodes bridging two or multiple modules. The plug-in has a detailed JAVA-based graphical interface with various colouring options. The ModuLand tool can run on Windows, Linux or Mac OS. We demonstrate its use on protein structure and metabolic networks.",

author = "M{\'a}t{\'e} Szalay-Beko and Robin Palotai and Bal{\'a}zs Szappanos and Kov{\'a}cs, {Istv{\'a}n A.} and Bal{\'a}zs Papp and P{\'e}ter Csermely",

note = "Funding Information: Funding: EU [FP6-518230, T{\'A}MOP-4.2.2/B-10/1-2010-0013 and FP7-264780]; Hungarian Scientific Research Fund [OTKA K-83314 and PD-75261]; International Human Frontiers Science Program Organization (BP); Momentum Program of the Hungarian Academy of Sciences (BP); and residence at the Rockefeller Foundation Bellagio Center (PC).",

year = "2012",

month = aug,

doi = "10.1093/bioinformatics/bts352",

language = "English (US)",

volume = "28",

pages = "2202--2204",

journal = "Bioinformatics",

issn = "1367-4803",

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T1 - ModuLand plug-in for Cytoscape

T2 - Determination of hierarchical layers of overlapping network modules and community centrality

AU - Szalay-Beko, Máté

AU - Palotai, Robin

AU - Szappanos, Balázs

AU - Kovács, István A.

AU - Papp, Balázs

AU - Csermely, Péter

N1 - Funding Information: Funding: EU [FP6-518230, TÁMOP-4.2.2/B-10/1-2010-0013 and FP7-264780]; Hungarian Scientific Research Fund [OTKA K-83314 and PD-75261]; International Human Frontiers Science Program Organization (BP); Momentum Program of the Hungarian Academy of Sciences (BP); and residence at the Rockefeller Foundation Bellagio Center (PC).

PY - 2012/8

Y1 - 2012/8

N2 - Summary: The ModuLand plug-in provides Cytoscape users an algorithm for determining extensively overlapping network modules. Moreover, it identifies several hierarchical layers of modules, where meta-nodes of the higher hierarchical layer represent modules of the lower layer. The tool assigns module cores, which predict the function of the whole module, and determines key nodes bridging two or multiple modules. The plug-in has a detailed JAVA-based graphical interface with various colouring options. The ModuLand tool can run on Windows, Linux or Mac OS. We demonstrate its use on protein structure and metabolic networks.

AB - Summary: The ModuLand plug-in provides Cytoscape users an algorithm for determining extensively overlapping network modules. Moreover, it identifies several hierarchical layers of modules, where meta-nodes of the higher hierarchical layer represent modules of the lower layer. The tool assigns module cores, which predict the function of the whole module, and determines key nodes bridging two or multiple modules. The plug-in has a detailed JAVA-based graphical interface with various colouring options. The ModuLand tool can run on Windows, Linux or Mac OS. We demonstrate its use on protein structure and metabolic networks.

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ModuLand plug-in for Cytoscape: Determination of hierarchical layers of overlapping network modules and community centrality

Abstract

Funding

ASJC Scopus subject areas

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