The GO terms "response to wounding" (GO:0009611) and "signal transduction" (GO:0007165) were enriched in the down-regulated probes of the LCLs (FDR P = 0.02, FDR P = 1.2*10-8) and the up-regulated probes of the PAX (FDR P = 0.002; FDR P = 0.001) and PBMCs (FDR P = 6.4*10-4; FDR P = 8.7*10-11). Hierarchical clustering of the variable weights of the 2,072 down- and up-regulated expression probes of all five methods resulted in clustering of transcripts according to these GO terms (Figure 4). To examine the concordance of gene expression measurements across methods, we extracted 1,952 expression probes that showed variable weights between -0.01 and 0.01 for all methods. GO analysis showed an enrichment of "secretion by cell" (GO:0032940: FDR P 3.2*10-3) and "antigen presentation and processing" (GO:0048000, FDR P = 0.02).
