WordCloud: a Cytoscape plugin to create a visual semantic summary of networks

The WordCloud Cytoscape plugin generates a visual summary of these annotations by displaying them as a tag cloud, where more frequent words are displayed using a larger font size. Word co-occurrence in a phrase can be visualized by arranging words in clusters or as a network.WordCloud provides a concise visual summary of annotations which is helpful for network analysis and interpretation. WordCloud is freely available at http://baderlab.org/Software/WordCloudPlugin webciteNetworks are widely used to represent relationships between biological entities, such as proteins and genes. Biological networks are typically explored using tools such as Cytoscape [1]. One common analysis consists of identifying sub-networks characterized by a specific feature, such as the presence of dense interconnections compared to the rest of the network [2]. For example, comprehensive maps of protein-protein physical interactions have been mined for dense regions, which represent protein complexes, using clustering algorithms [3]. Once sub-networks have been identified, however, it is often difficult to interpret their biological meaning. Bio-entities typically have rich textual information associated with them, such as Gene Ontology (GO) annotations [4]. A popular method for interpreting sub-networks using this information is enrichment analysis, where node and edge attributes are mined for statistically enriched text terms. For example, a sub-network can be searched for enriched biological pathways associated with the list of nodes. While highly useful, enrichment analysis takes time to perform and produces a simple table of enriched attributes. When deciding which sub-networks are interesting, it is useful to have quick visual feedback displaying frequent node annotation. In previous work, we manually created 'word clouds' to help us with this task [5]. The purpose of the WordCloud plugin is to automatically generate concise visual summaries of such textual attributes for fast access du