Physics – Computational Physics
Scientific paper
2011-11-13
Physics
Computational Physics
20 pages, 1 figure and a Supplement with 6 figures and 7 tables
Scientific paper
Summary: The extensively overlapping structure of network modules is an increasingly recognized feature of biological networks. Here we introduce a user-friendly implementation of our previous network module determination method, ModuLand, as a plug-in of the widely used Cytoscape program. We show the utility of this approach a.) to identify an extensively overlapping modular structure; b.) to define a modular core and hierarchy allowing an easier functional annotation; c.) to identify key nodes of high community centrality, modular overlap or bridgeness in protein structure, protein-protein interaction and metabolic networks. Availability and implementation: The ModuLand Cytoscape plug-in was written in C++, has a JAVA-based graphical interface, can be installed as a single plug-in and can run on Windows, Linux, or Mac OS. The plug-in and its user guide can be downloaded from: http://www.linkgroup.hu/modules_bioinfo_download.php
Csermely Peter
Kovacs Istvan A.
Palotai Robin
Papp Balazs
Szalay-Beko Mate
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