Fig. 5
From: ADAGE signature analysis: differential expression analysis with data-defined gene sets
The gene-gene network for the example dataset. a The ADAGE gene-gene network subset by genes in the selected active signatures. Each vertex in the network is a gene. Vertex color corresponds to gene expression fold change between ∆anr mutant and wild-type (red: high in ∆anr mutant; blue: low in ∆anr mutant). Genes with black border are genes that have KEGG pathway annotations. The thickness of edges reflects how strong gene-gene relationships are in the ADAGE model. b The network module of genes in Node35pos. c The network module of genes involved in denitrification