GeneMANIA (Warde-Farley et al., 2010) (genmania.org), a tool for functional gene analysis, was used for co-expression analysis. Default parameter values were used except “max resultant genes” was set to zero to limit the analysis to those genes supplied in the list. GeneMANIA identifies the genes most related to a query gene set using a guilt-by-association approach, based upon a large database of publicly available functional interaction networks. For co-expression networks, two genes are linked if their expression levels are similar across conditions in a gene expression study; GeneMANIA weights this across data from multiple organisms, cell-types and tissues. Data from Cahoy et al., 2008, was used to identify genes enriched in astrocytes, oligodendrocytes and neurons. Designation as “enriched” was limited to genes having at least a 1.5-fold enrichment in one of the three cells types compared to the other cells. The proportions test in R (https://cran.r-project.org/) was used to determine if there was a significant difference in the percentage of genes decreased in each of the three cell types compared to the percentage decreased among all differentially expressed genes.
