Enrichments of co-annotated genes among the differentially expressed genes.

Differentially expressed gene sets were compared to Gene Ontology biological process annotations [50] and KEGG pathway annotations [51] using the hypergeometric distribution and corrected for multiple testing using the Benjamini and Hochberg FDR method [52]. They were also compared to two brain cell type-specific gene expression datasets [21], [53] which refer to GEO accessions GSE9566 and GSE13379. For each dataset, we first clustered the gene expression patterns using CLICK [22], manually annotated each cluster based on each expression pattern; and then tested the significance of the overlap between each set of differentially expressed genes in our data and each co-expression cluster using the hypergeometric test. Full gene lists of enrichment results are presented in File S2.