The 4th strongest association (q-value = 2.03e−20) in our analysis showed that the presence of G163 (found in 8% of sequences) was associated with the S165N mutation (found in 9% of sequences), demonstrating that our method identifies associations between deleterious and compensatory mutations.
In contrast, TAg re-localized to nuclear inclusions in cells expressing p53-IC (Figure 7A, bottom row), demonstrating that our method is able to detect the interaction of plasmid-expressed p53 with endogenous TAg in the nucleus of COS-7 cells.
Supplementary Materials Figure S1 shows that the histogram is close to uniform distributions, demonstrating that our method successfully controls the rate of false positives.
The TPR values of the SIG method are much higher than those of other two methods, demonstrating that our method is more effective in selecting biologically relevant gene pairs.
Families in our test set exhibit a broad range of domain architectures and sequence conservation, demonstrating that our method is flexible, robust and suitable for high-throughput, automated processing of heterogeneous, genome-scale data.
In the youngest strata, where all methods are expected to perform equally well, our predictions reconciled well with predictions from existing methods that require Y homology, demonstrating that our method can be reliably used to identify evolutionary strata in the absence of sequence information from the heterogametic sex chromosome.
