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

Bioinformatics. 2012 Aug 15;28(16):2202-4. doi: 10.1093/bioinformatics/bts352. Epub 2012 Jun 19.

Authors

Máté Szalay-Beko¹, Robin Palotai, Balázs Szappanos, István A Kovács, Balázs Papp, Péter Csermely

Affiliation

¹ Department of Medical Chemistry, Semmelweis University, Budapest 1444, Hungary.

PMID: 22718784
DOI: 10.1093/bioinformatics/bts352

Abstract

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.

Availability: The plug-in and its user guide can be downloaded freely from: http://www.linkgroup.hu/modules.php.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Color
Computational Biology / methods
Metabolic Networks and Pathways*
Protein Interaction Maps
Proteins / chemistry*
Software*
User-Computer Interface*

Substances

Proteins