To robustly calculate the gene-gene correlations, hdWGCNA (0.2.02)74 was used by grouping transcriptionally similar cells in each replicate and sub-cluster of Microglia from EAE CD83wtCre condition. To remove noise, “TestSoftPower” was used to determine the value to which the correlations were increased. The resulting correlation matrix was used to extract the correlation values of all genes with Cd83 and the top ten percent of those genes with higher correlation values were selected as highly correlating with Cd83 and subjected to functional enrichment analysis.
