Figure 2

Annotation of the up- and down-regulated modules. a) The up-regulated priming and acute activation modules are distinct. The main up-regulated modules (blue modules for priming datasets and red for the acute dataset) were annotated with Webgestalt to determine significantly enriched KEGG-pathways and Gene Ontologies. These results are depicted with the multiple testing (FDR) corrected p-values. Using the UserListEnrichment function, significance was calculated for the overlap between these modules and gene sets significantly up-regulated in macrophages stimulated with IL-4, IFN? or LPS, and microglia-aging profile. For the UserlistEnrichment results Bonferroni multiple-testing p values are shown. b) KEGG-GO and UserlistEnrichment annotation of the down-regulated modules. The main down-regulated modules (dark-green modules for priming datasets and green-yellow for the acute dataset) were annotated with Webgestalt to determine significantly enriched KEGG-pathways and Gene Ontologies. These results were depicted as a table with multiple testing (FDR) corrected p-values. Using the UserListEnrichment function, significance was calculated for the overlap between these modules and the Butovsky microglia-signature [36]. For the UserlistEnrichment results Bonferroni multiple-testing p values are shown. c) KEGG-GO annotation of mouse model specific modules The Ercc1 down-regulated magenta module and ALS dark-turquoise up-regulated module were GO annotated, multi-testing (FDR) corrected p values are depicted.