Visualization features, such as the enriched DAG (directly acyclic graph) for revealing the hierarchical relationship of enriched GO terms, have been the most appreciated features in WebGestalt according to feedback from our users. In the updated version, enriched DAG visualization has been applied to the phenotype enrichment results for visualizing the hierarchical relationship of enriched phenotype terms. Because our newly defined protein interaction network modules also have a hierarchical organization, we have extended the enriched DAG visualization to present results from network module enrichment analysis (Figure 2A). The enriched DAG shows enriched network modules in red and their non-enriched parents in black. As shown in Figure 2A, enriched modules could be found at different hierarchical levels. Therefore, using only gene sets derived from a single-level decomposition of a network may miss important functional information encoded in the network. Unlike GO categories in which relationship among genes is not defined, relationship among genes in a network module is well-defined by the network graph. To reveal this additional level of information, WebGestalt uses the Cytoscape Web (25) plug in to visualize in
