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Bioinformatics Advance Access originally published online on October 4, 2006
Bioinformatics 2006 22(23):2968-2970; doi:10.1093/bioinformatics/btl488
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks

Kevin Y. Yip 1, Haiyuan Yu 2, Philip M. Kim 3, Martin Schultz 1 and Mark Gerstein 1,3,*

1 Department of Computer Science, Yale University 51 Prospect Street, New Haven, CT 06511, USA
2 Department of Cancer Biology, Dana-Farber Cancer Institute 1 Jimmy Fund Way, SM854, Boston, MA 02115, USA
3 Department of Molecular Biophysics and Biochemistry, Yale University 266 Whitney Avenue, New Haven, CT 06520, USA

*To whom correspondence should be addressed.

Summary: Biological processes involve complex networks of interactions between molecules. Various large-scale experiments and curation efforts have led to preliminary versions of complete cellular networks for a number of organisms. To grapple with these networks, we developed TopNet-like Yale Network Analyzer (tYNA), a Web system for managing, comparing and mining multiple networks, both directed and undirected. tYNA efficiently implements methods that have proven useful in network analysis, including identifying defective cliques, finding small network motifs (such as feed-forward loops), calculating global statistics (such as the clustering coefficient and eccentricity), and identifying hubs and bottlenecks. It also allows one to manage a large number of private and public networks using a flexible tagging system, to filter them based on a variety of criteria, and to visualize them through an interactive graphical interface. A number of commonly used biological datasets have been pre-loaded into tYNA, standardized and grouped into different categories.

Availability: The tYNA system can be accessed at http://networks.gersteinlab.org/tyna. The source code, JavaDoc API and WSDL can also be downloaded from the website. tYNA can also be accessed from the Cytoscape software using a plugin.

Contact: mark.gerstein{at}yale.edu

Supplementary information: Additional figures and tables can be found at http://networks.gersteinlab.org/tyna/supp

Received on June 30, 2006; revised on August 25, 2006; accepted on September 15, 2006

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