Fig. 6

GSEA identifies unique gene expression patterns in Gch1 cells. Gene expression data from both Gch1 and Nos2 deficient macrophages were analysed for GO term (biological processes) enrichment by Preranked gene-set enrichment analysis (GSEA) vs their wildtype control. The result was visualized as a network of gene sets (nodes) connected by their similarity (edges), compiled in Cytoscape using the Enrichment Map plug in. Node size represents the gene-set size and edge thickness represents the degree of overlap between neighboring gene sets. The GSEA output files were given analysed with a statistical cutoff set at p < 0.005 and FDR q < 0.1. The individual Enrichment Maps were plotted in Cytoscape for infected a Gch1 and b Nos2 macrophages and clusters were annotated by hand. To determine if regulated genesets were shared between the Gch1 and Nos2 knockout macrophages the significantly regulated gene sets were compared and a subset of genesets unique to Gch1 deficient macrophages was created, this subset (c) was plotted using Enrichment Map and the clusters annotated. d A table summarizing the GO-term clusters, with exemplar GO terms