Table 2. Summary for modeling outlier sites in six cancer types.
Table 2—source data 1. The outlier model parameters and expected Si values for 6 cancer types analyzed.
‘pMinor’ and ‘alpha’ correspond to (‘p, a’) as described in the main text. ‘Eu’ represents the average mutation rate per site per patient for the given cancer type (‘ccType’). ‘s2Expt’ ‘s3Expt’ ‘4’ ‘s5’ and ‘s6’ are the expected Si values for i = 2, 3, 4, 5, 6, respectively. ‘s2Obsv’ and ‘s3Obsv’ represent the observed Si values for S2 and S3.
elife-99340-table2-data1.zip (47MB, zip)
| Cancer Type | S3 | p | α | S4 | S5 |
|---|---|---|---|---|---|
| Lung* | -- | 0.0 | -- | -- | -- |
| Breast | 0.12 | 8.75E-04 (8.21E-04) | 88.6 (32.0) | 0.102 (0.068) | 0.004 (0.004) |
| CNS | 0.02 | 2.73E-04 (1.09E-04) | 295.1 (57.0) | 0.448 (0.173) | 0.026 (0.015) |
| Kidney | 0.03 | 3.03E-05 (2.98E-05) | 304.1 (108.0) | 0.067 (0.056) | 0.005 (0.006) |
| Upper-AD tract | 0.47 | 0.002 (0.001) | 48.9 (10.7) | 0.174 (0.078) | 0.005 (0.003) |
| Large intestine | 1.03 | 0.009 (0.001) | 51.6 (1.4) | 0.998 (0.087) | 0.026 (0.003) |
Note – For each cancer type, p stands for the proportion of highly mutable sites, with mutation rate being α-fold of the average. S3 gives the expected number without mutable outliers (P=0). S4 and S5 denote the expected number with the best (p, α) pairs with the standard deviation in parentheses. For lung cancer, S2 and S3 do not fit the outlier model (Table 2—source data 1); therefore, we set P=0.