Phenotype-based gene sets from the Mammalian Phenotype Ontology that are significantly enriched for genes associated with carnivory score
| Phenotype | Enrichment statistic | Parametric P-value | Parametric Q-value | Permulation P-value | Permulation Q-value |
|---|---|---|---|---|---|
| MP:0002223 lymphoid hypoplasia | −0.304 | 8.60 × 10−4 | 0.076 | <7.00 × 10−5 a | <0.057a |
| MP:0003949 abnormal circulating lipid level | −0.235 | 3.30 × 10−5 | 0.011 | 7.00 × 10−5 | 0.057 |
| MP:0001547 abnormal lipid level | −0.170 | 3.62 × 10−9 | 1.20 × 10−5 | 8.00 × 10−5 | 0.057 |
| MP:0005441 increased urine calcium level | −0.311 | 7.74 × 10−8 | 8.53 × 10−5 | 8.00 × 10−5 | 0.057 |
| MP:0002988 decreased urine osmolality | −0.181 | 1.01 × 10−5 | 0.006 | 8.00 × 10−5 | 0.057 |
[i] Permulation P-values represent the proportion of 100,000 permulations that produced a stronger enrichment statistic than the observed value for each gene set. Multiple hypothesis testing corrections were performed by generating Q-values using Storey's correction method (Storey et al. 2020) (FDR = 0.1). A negative enrichment statistic signifies the following pattern: the greater the decrease in carnivory, the higher the rate of evolution of the gene.
[ii] aAfter generating 100,000 null statistics, none produced a stronger correlation with diet than the observed values for MP:0002223. However, if the P-values are adjusted to the smallest observed nonzero P-value (7.00 × 10−5), they would produce a significant empirical Q-value (FDR = 0.1).