To validate whether this increase in co-expressed transcripts reflects known biology, we assessed a collection of 80,350 known biological interactions (derived on 17 April 2007 from KEGG [33], BioGrid [34], Reactome [35], BIND [36], HPRD [37] and IntAct [38]). For the celiac peripheral blood dataset 91 of the 50,821 (0.179%) significantly correlated transcript-pairs that had been identified in the unconditioned co-expression analysis are known to interact. In the conditioned co-expression analysis 106 of the 54,773 (0.194%) transcript pairs were known to interact, indicating an 8.0% increase in the proportion of known biological interactions that was identified. Comparable results were obtained for the HapMap B cell line dataset: For the unconditioned co-expression analysis 334 of the 168,292 (0.195%) significant transcript-pairs are known to interact. In the conditioned co-expression analysis 634 of the 258.874 (0.245%) significant transcript-pairs are known to biologically interact, representing an increase of 23.4% in the proportion of known interactions among the most significantly co-expressed transcript-pairs.
