To identify differentially expressed genes between individuals with high or low lymphocyte counts, we employed a likelihood ratio test within the framework of a fixed-effect linear model (see Materials and Methods for more details). Using this approach, we classified 33 genes as differentially expressed between the two groups (FDR = 10%; Supplementary Material, Table S3). While the set of genes identified as differentially expressed is small, it is enriched with genes involved in relevant functions based on Gene Ontology (GO) classifications, such as ‘alpha-beta T cell differentiation’, and ‘alpha-beta T cell activation’ (at an FDR < 0.04; Supplementary Material, Table S4). We found enrichment of similar functions (including: ‘alpha-beta T cell receptor complex’, ‘T cell receptor complex’ and ‘T cell activation’; see Supplementary Material, Table S5), even when we extended our analysis to the 200 genes with the best evidence for differences in expression levels between individuals with high or low lymphocyte counts (P < 0.005). This observation indicates that, much like the GWAS results, our study is underpowered to identify all genes whose regulation is associated with lymphocyte counts.
