Figure 1.
PCA was performed using pair-wise sample covariance matrix of 187 samples and applied to the genome-wide gene expression data (10,313 genes detected as expressed). Filled circles correspond to original hybridization and empty circles correspond to technical hybridization replicates (samples that were hybridized in more than one array batch).
Figure 2.
Relative EBV copy numbers in LCLs from six individuals.
Error bars indicate the standard error of the mean.
Figure 3.
Individual effect on gene expression patterns.
PCA was applied to the genome-wide expression data of A) cycle 0 and cycle 2 B) cycle 0 and cycle 4 C) cycle 0 and cycle 6 LCL cultures. Numbers correspond to the individual origin of the culture (of the six individuals).
Figure 4.
Gene expression variation in mature LCLs can observe only a fraction of the inter-individual variation in gene expression levels that exists in the primary B cells.
A) Density distributions of the coefficient of variation (CV) of gene expression between-individuals within primary B cells and within LCLs of each freeze-thaw cycle. Black vertical line designates the arbitrarily chosen threshold of CV of 0.025. B) Bar plots showing the numbers of genes classified as having ‘highly variable’ expression patterns in the primary B cells, cycle 0, cycle 2, cycle 4, and cycle 6 LCLs. C) Venn diagram of the overlaps in genes with ‘highly variable’ expression patterns across primary B cells, cycle 0, cycle 2, cycle 4, and cycle 6 LCLs. We also plotted an equivalent figure based on residual data after regressing out mtDNA and EBV copy numbers; see Figure S10 in in Appendix S1.
Figure 5.
Previously identified eQTLs are enriched among the genes whose regulations in mature LCLs maintain marked inter-individual variation.
A) Bar plots showing the percent of genes with eQTLs (as identified in LCL-Study 5) among all genes detected as expressed and among genes with ‘highly variable’ expression patterns in B cells, cycle 0, cycle 2, cycle 4, and cycle 6 LCLs. Asterisks indicate that the null hypothesis of no difference in proportion of genes with eQTLs relative to that in all expressed genes was rejected at P values <8.3×10−4 (Bonferroni corrected significance threshold). Results pertaining to all twelve eQTL studies are included in Figure S8 and Table S8 in Appendix S1. B) Mean coefficient of variation (CV) of gene expression within each cell type/freeze-thaw cycle for all the genes detected as expressed and for genes with eQTLs (as identified in LCL Study-5). Results for all twelve eQTL studies are included in Figure S9 and Table S9 in Appendix S1.
Table 1.
The list of eQTL studies whose results were downloaded from the Pritchard Lab eQTL browser (eqtl.uchicago.edu).