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Bioinformatics Advance Access originally published online on September 2, 2009
Bioinformatics 2009 25(21):2857-2859; doi:10.1093/bioinformatics/btp517
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Analyzing biological network parameters with CentiScaPe

Giovanni Scardoni 1,*, Michele Petterlini 1 and Carlo Laudanna 1,2

1 Center for Biomedical Computing, University of Verona, Strada le Grazie, 15 -37134 Verona and 2 Department of Pathology, University of Verona, Strada le Grazie, 8 – 37134 Verona, Italy

* To whom correspondence should be addressed.


  Abstract

Summary: The increasing availability of large network datasets along with the progresses in experimental high-throughput technologies have prompted the need for tools allowing easy integration of experimental data with data derived form network computational analysis. In order to enrich experimental data with network topological parameters, we have developed the Cytoscape plug-in CentiScaPe. The plug-in computes several network centrality parameters and allows the user to analyze existing relationships between experimental data provided by the users and node centrality values computed by the plug-in. CentiScaPe allows identifying network nodes that are relevant from both experimental and topological viewpoints. CentiScaPe also provides a Boolean logic-based tool that allows easy characterization of nodes whose topological relevance depends on more than one centrality. Finally, different graphic outputs and the included description of biological significance for each computed centrality facilitate the analysis by the end users not expert in graph theory, thus allowing easy node categorization and experimental prioritization.

Availability: CentiScaPe can be downloaded via the Cytoscape web site: http://chianti.ucsd.edu/cyto_web/plugins/index.php. Tutorial, centrality descriptions and example data are available at: http://profs.sci.univr.it/~scardoni/centiscape/centiscapepage.php

Contact: giovanni.scardoni{at}gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Alfonso Valencia

Received on February 11, 2009; revised on August 5, 2009; accepted on August 24, 2009

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