![]() ClueGO takes advantage of Cytoscape's versatile visualization framework and can be used in conjunction with the GOlorize plug-in (Garcia et al., 2007). In addition, ClueGO can compare clusters of genes and visualizes their functional differences. A variety of flexible restriction criteria allow for visualizations in different levels of specificity. ClueGO integrates GO terms as well as KEGG/BioCarta pathways and creates a functionally organized GO/pathway term network. ( 2008) which creates an in silico annotation network based on pathways and protein interaction data and maps the gene list of interest afterwards, ClueGO generates a dynamical network structure by already initially considering the gene lists of interest. Compared with the approach of Ramos et al. Other tools like BiNGO (Maere et al., 2005) or PIPE (Ramos et al., 2008) assess overrepresented GO terms and reconstruct the hierarchical ontology tree, whereas ClueGO uses kappa statistics to link the terms in the network. Li et al., 2008) were developed to enhance data interpretation.Īs most of these tools mainly present their results as long lists or complex hierarchical trees, we aimed to develop ClueGO a Cytoscape (Shannon et al., 2003) plug-in to facilitate the biological interpretation and to visualize functionally grouped terms in the form of networks and charts. Boyle et al., 2004 Huang et al., 2007 Maere et al., 2005 Ramos et al., 2008 Zeeberg et al., 2003) and algorithms (e.g. Several functional enrichment analysis tools (e.g. For example Gene Ontology (GO) (Ashburner et al., 2000) annotates genes to biological/cellular/molecular terms in a hierarchically structured way, whereas Kyoto encyclopedia of genes and genomes (KEGG) (Kanehisa et al., 2002) and BioCarta assigns genes to functional pathways. Since the number of genes that can be analyzed by high-throughput experiments by far exceeded what can be interpreted by a single person, different attempts have been initiated in order to capture biological information and systematically organize the wealth of data.
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