Fig. 2

Visualizations of functional enrichment and interactome analysis results. a Screenshot of a portion of the directed acyclic graph rendered by Babelomics⁵³ based on enriched GO terms. b Screenshot of a portion of the gene-term association matrix rendered by g:profile⁴², where enriched GO terms are organized hierarchically. c Screenshot of a portion of the tabular display of enriched terms rendered by DAVID based on all GO terms, KEGG pathways, Reactome, and CORUM. The terms related to “viral gene expression” were missed in the visualizations generated by Babelomics and g:profile, but were identified by DAVID (in cluster 8 with ranks around 20). d Metascape bar graph for viewing top non-redundant enrichment clusters, one per cluster, using a discrete color scale to represent statistical significance. e Metascape enrichment network visualization showing the intra-cluster and inter-cluster similarities of enriched terms, up to ten terms per cluster. Cluster annotations are shown in color code. f A complex interactome network generated by g:profile with the Brass gene list. g Metascape visualization of the interactome network formed by all 121 gene candidates from the Brass list, where the MCODE complexes are colored according to their identities. h Seven MCODE complexes automatically identified in Metascape, colored by their identities. Their functional labels are generated based on the top-three functional enriched terms, if available