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

Abstract

Background: When biological networks are studied, it is common to look for clusters, i.e. sets of nodes that are highly inter-connected. To understand the biological meaning of a cluster, the user usually has to sift through many textual annotations that are associated with biological entities.

Findings: 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.

Conclusions: 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.

Figure 1

Tag cloud for a protein interaction cluster. The network consists of physical interactions between S. cerevisiae proteins involved in DNA replication (A). A group of highly inter-connected proteins was selected (blue circle) and their full names were mined using WordCloud. The results are shown for the three layouts: network (B), simple (C) and clustered (D). "Origin recognition complex component" and "Minichromosome maintenance complex component" are the dominating themes. The corresponding words are ranked on top in the simple cloud layout, but only the clustered and network layout reconstruct the correct connections between them, based on word co-occurrence patterns. Since clustering is non-overlapping, the words "complex" and "component" are forced to appear only in one cluster (with "minichrosome maintenance"), whereas the network layout displays association to "origin recognition" as well.

Figure 2

Application of WordCloud to gene-set enrichment analysis results. The transcriptional response of breast cancer cells to estrogen treatment was analyzed for gene-set enrichment, as described in [11]. Gene-sets were then arranged as a network using the Enrichment Map visualization technique [11]; edges represent gene-set overlap and clusters correspond to functional groups. A sub-network (A) was selected and analyzed using the WordCloud network layout (B). The most frequent words in gene-set names are "Mitotic Cell Cycle", "DNA Replication", "Ubiquitin Ligase Activity/Regulation", "Chromosome", "Microtubule"; this suggests that the sub-network consists of gene-sets involved in the control of cell proliferation. Specific parts of the sub-network (purple circles) relate to specific functional groups, as suggested by clustered word clouds (C,D).