Table 1 Correlations between median expression distance and regulatory similarity. The performance of different distance measures were compared in each of seven mouse experiments: Su et al. (Su), Storch et al. (Circadian), the neocortex development (Cortex), the murine model of human asthma (Lung), the hippocampus samples from neurofibromin-1 heterozygous study (NF), Zhao et al. (Muscle), and Wang et al.(PI). The number of microarrays used in each data set are shown in the first row. The p-values in the parentheses are obtained by permuting the mapping between genes and their promoter regions 500 times.
Expression distance measure | Su 89 | Circadian 24 | Cortex 17 | Lung 39 | NF 30 | Muscle 54 | PI 35 |
|---|---|---|---|---|---|---|---|
1 – correlation | -0.165 (0.422) | -0.261 (0.158) | -0.636 (0.008) | -0.423 (0.124) | -0.826 (0.000) | -0.358 (0.170) | -0.384 (0.198) |
1 – cosine correlation | -0.802 (0.000) | -0.392 (0.106) | -0.679 (0.002) | -0.456 (0.066) | -0.878 (0.000) | -0.047 (0.488) | 0.016 (0.666) |
Square root 1 – correlation | -0.177 (0.416) | -0.280 (0.230) | -0.636 (0.008) | -0.412 (0.162) | -0.836 (0.000) | -0.401 (0.148) | -0.396 (0.200) |
Square root 1 – cosine correlation | -0.783 (0.000) | -0.401 (0.166) | -0.683 (0.002) | -0.464 (0.064) | -0.869 (0.000) | -0.104 (0.490) | -0.007 (0.670) |
1 – correlation after log2 transformation | -0.178 (0.310) | -0.254 (0.124) | -0.459 (0.032) | -0.534 (0.030) | -0.798 (0.000) | -0.136 (0.314) | -0.035 (0.428) |
1 – cosine correlation after log2 transformation | -0.685 (0.006) | -0.026 (0.346) | -0.833 (0.000) | -0.830 (0.000) | -0.874 (0.000) | -0.540 (0.032) | 0.346 (0.812) |
The new distance measure | -0.777 (0.000) | -0.789 (0.000) | -0.735 (0.002) | -0.776 (0.000) | -0.859 (0.000) | -0.774 (0.000) | -0.656 (0.000) |