FIGURE 3 

Two measurements of the quality of the derived physical protein associations. (A) The cumulative log likelihood ratio (LLR) of physically associating, measured with an independent test set of 15 810 human protein physical associations, plotted as a function of the number of associations. The CCE associations are significantly more enriched for known physical associations than randomized protein pairs or those derived only from human mRNA co-expression. The left y axis indicates the LLR score for the associations based on comparison to the known interaction test set; the right y axis indicates the corresponding likelihood ratio. Associations were ranked by confidence (see Materials and methods) and binned into sets of 1000 associations per bin for analysis. (B) The tendency for putative interaction partners to participate in the same pathway. The left y axis indicates the cumulative LLR (and the right y axis the corresponding likelihood ratio) for interaction partners to belong to the same pathway, using the same log likelihood framework as in (A), but employing as a positive test set the 1.5 million human protein pairs defined in the GO and KEGG databases as belonging to the same pathway. As in (A), CCE associations are comparable in quality to literature associations and score significantly higher than randomized associations and those derived using only human expression data.