eXamine : a Cytoscape app for exploring annotated modules in networks

K. Dinkla, M. El-Kebir, C.-I. Bucur, M. Siderius, M.J. Smit, M.A. Westenberg, G.W. Klau

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Background. Biological networks have growing importance for the interpretation of high-throughput "omics" data. Statistical and combinatorial methods allow to obtain mechanistic insights through the extraction of smaller subnetwork modules. Further enrichment analyses provide set-based annotations of these modules. Results. We present eXamine, a set-oriented visual analysis approach for annotated modules that displays set membership as contours on top of a node-link layout. Our approach extends upon Self Organizing Maps to simultaneously lay out nodes, links, and set contours. Conclusions. We implemented eXamine as a freely available Cytoscape app. Using eXamine we study a module that is activated by the virally-encoded G-protein coupled receptor US28 and formulate a novel hypothesis about its functioning.
Original languageEnglish
Number of pages15
Publication statusPublished - 2013

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