Comparison of H1 and DHHE and HHP and HHE for KEGG proteins. The upper half of the figure compares direct predictions (H1) with experimentally verified direct interactions (DHHE) for ENV, NEF and TAT. The p-values indicated a significant overlap for all protein sets. The bottom half of the figure compares HHP and HHE for the three HIV-1 proteins when HHP was restricted to genes in all KEGG pathways (ENVa, NEFa, TATa), and KEGG pathways enriched (p-value < 0.01, see Methods) with HHP (ENVe, NEFe, TATe). The intersection between HHP and HHE was significant for both projections, but slightly more significant for enriched pathways for ENV and NEF. P-values were calculated as described in Methods.