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. 2010 May 1;26(9):1271-2.
doi: 10.1093/bioinformatics/btq131. Epub 2010 Mar 24.

TopoGSA: network topological gene set analysis

Enrico Glaab  1 , Anaïs Baudot, Natalio Krasnogor, Alfonso Valencia
Affiliations

TopoGSA: network topological gene set analysis

Enrico Glaab et al. Bioinformatics. .

Abstract

TopoGSA (Topology-based Gene Set Analysis) is a web-application dedicated to the computation and visualization of network topological properties for gene and protein sets in molecular interaction networks. Different topological characteristics, such as the centrality of nodes in the network or their tendency to form clusters, can be computed and compared with those of known cellular pathways and processes.

Availability: Freely available at http://www.infobiotics.net/topogsa.

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Figures

Fig. 1.
Fig. 1.
Example results produced with TopoGSA based on the cancer gene set by Futreal et al. (2004). (a) Topological properties can be computed and examined as visual (1) and tabular (2) outputs; (b) The gene set can be compared with a chosen reference database (here the KEGG database).
See this image and copyright information in PMC

References

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    1. Bader G, et al. BIND–the biomolecular interaction network database. Nucleic Acids Res. 2001;29:242–245. - PMC - PubMed
    1. Bonacich P, et al. Eigenvector-like measures of centrality for asymmetric relations. Soc. Networks. 2001;23:191–201.

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