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

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, w...

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Bibliographic Details
Published in:Bioinformatics 2012-08, Vol.28 (16), p.2202-2204
Main Authors: SZALAY-BEKO, Mate, PALOTAI, Robin, SZAPPANOS, Balázs, KOVACS, István A, PAPP, Balázs, CSERMELY, Peter
Format: Article
Language:English
Subjects:
Algorithms
Biological and medical sciences
Color
Computational Biology - methods
Fundamental and applied biological sciences. Psychology
General aspects
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Metabolic Networks and Pathways
Protein Interaction Maps
Proteins - chemistry
Software
User-Computer Interface
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Description
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. The plug-in and its user guide can be downloaded freely from: http://www.linkgroup.hu/modules.php.
ISSN:1367-4803
1367-4811
1460-2059
DOI:10.1093/bioinformatics/bts352