Analyzing biological network parameters with CentiScaPe

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/ approximately scardoni/centiscape/centiscapepage.php

Contact: giovanni.scardoni@gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.

Fig. 1.

Network analysis of human kino-phosphatome. (A) The protein kinase MAPK1 shows high centralities values for most of the computed centralities suggesting its central role in the network structure and function. For each centrality the specific node value (gray), the mean value (black), the min value (light gray) and the max value (white) is shown. (B) The correlations between centroid value and intensity of protein phosphorylation in Tyrosine. Proteins with high centroid value and high level of phosphorylation are easily identified in the top/right quadrant of the graph. Pointing the mouse over the geometrical shapes in the plot shows the corresponding node ID and attribute values (see Section 3 and Supplementary Materials).