Table 2.
Summary of correlation results between ovarian gene expression and phenotypes
| Trait | Correlated clonesa | Trait interactionsb | Direction and strength of correlation (R value range)c | Gene expression shift (δ log2 value range)d | |||||
|---|---|---|---|---|---|---|---|---|---|
| OTF | NL | LS | RF | Positive | Negative | Positive | Negative | ||
| Ovarian tumor frequency (OTF) | 425 (280) | - | 145 | 0 | 0 | 97 (1.00-0.51) | 328 (1.00-0.52) | 3.26 - 0.19 | 2.96 - 0.21 |
| Number of litters (NL) | 234 (82) | 145 | - | 0 | 7 | 161 (1.00-0.73) | 72 (0.99-0.67) | 2.94 - 0.32 | 3.00 - 0.24 |
| Litter size (LS) | 73 (66) | 0 | 0 | - | 7 | 53 (0.99-0.78) | 20 (0.99-0.62) | 2.50 - 0.32 | 2.18 - 0.41 |
| Relative fecundity (RF) | 17 (3) | 0 | 7 | 7 | - | 12 (0.98-0.78) | 5 (0.98-0.90) | 1.50 - 0.29 | 0.85 - 0.51 |
a Number of clones resulting from a regression analysis with false discovery rate (FDR) control performed with the multiple test tool Pomelo (accessible at http://pomelo2.bioinfo.cnio.es/). For each trait, genes were filtered with an adjusted p<0.05 resulting in a total of 590 unique arrayed clones showing statistically significant correlation. Under this criterion, the trait “productive matings” did not show correlation. The number of clones exclusively correlated with the indicated trait is shown between parentheses.
b Interactions correspond to the number of clones correlated with two or more traits as obtained with Boolean comparisons.
c Pearson correlation coefficients (R) were calculated using gene expression log2 ratios as independent variable and each of phenotypic trait (see Table 1) as dependent variables. The observed range of R values for all correlated genes is shown between parentheses.
d Gene expression ratios (log2) for the extreme trait values were subtracted (δ) and then ranked. The highest and the lowest ratio difference are shown between parentheses.