Table 3 NOD2 GenePy score statistics (maxima and means) and Mann-Whitney U tests across groups for all sixteen deleteriousness metrics. p-values smaller than 1 × 10−2 or smaller than 5 × 10−2 are highlighted by two (**) or one (*) asterisks respectively. SKAT-O gene association results comparing patient groups against controls provided below thick line
Metric | Controls (n = 166) | IBD (n = 282) | UC (n = 100) | CD (n = 172) | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
max | mean | max | mean | Mann-Whitney U comparison against controls | max | mean | Mann-Whitney U comparison against controls | max | mean | Mann-Whitney U comparison against controls | |
CADD | 2.71 | 0.28 | 3.52 | 0.40 | 1.04 × 10−1 | 2.66 | 0.20 | 1.38 × 10−1 | 3.52 | 0.54 | 4.62 × 10−4 ** |
DANN | 5.92 | 0.84 | 7.62 | 1.06 | 1.36 × 10−1 | 5.62 | 0.57 | 1.22 × 10−1 | 7.62 | 1.38 | 8.16 × 10− 4 ** |
FATHMM | 3.33 | 0.49 | 4.34 | 0.66 | 1.04 × 10−1 | 3.14 | 0.38 | 1.47 × 10− 1 | 4.34 | 0.84 | 4.84 × 10− 4 ** |
fathmm-MKL | 4.53 | 0.37 | 6.24 | 0.55 | 4.54 × 10−2 * | 3.78 | 0.25 | 3.15 × 10− 1 | 6.24 | 0.76 | 1.79 × 10− 4 ** |
GERP++_RS | 5.30 | 0.64 | 7.00 | 0.87 | 1.26 × 10− 1 | 4.95 | 0.42 | 1.27 × 10− 1 | 7.00 | 1.17 | 6.95 × 10− 4 ** |
M-CAP | 1.87 | 0.12 | 3.39 | 0.22 | 1.58 × 10− 2 * | 1.73 | 0.08 | 4.62 × 10− 1 | 3.39 | 0.32 | 1.37 × 10− 4 ** |
MetaLR | 2.42 | 0.16 | 3.39 | 0.29 | 2.71 × 10− 1 | 1.81 | 0.10 | 2.34 × 10− 2 * | 3.39 | 0.42 | 1.63 × 10−3 ** |
MetaSVM | 2.67 | 0.30 | 3.61 | 0.43 | 9.88 × 10− 2 | 2.50 | 0.22 | 1.50 × 10− 1 | 3.61 | 0.57 | 4.39 × 10− 4 ** |
MutationTaster | 4.38 | 0.26 | 5.10 | 0.39 | 4.48 × 10− 2 * | 2.65 | 0.13 | 4.37 × 10− 1 | 5.10 | 0.57 | 7.47 × 10− 4 ** |
phastCons | 4.66 | 0.35 | 5.24 | 0.56 | 2.86 × 10− 1 | 3.54 | 0.24 | 2.70 × 10− 2 * | 5.24 | 0.77 | 2.16 × 10− 3 ** |
phyloP | 6.32 | 1.02 | 7.93 | 1.27 | 1.23 × 10− 1 | 5.92 | 0.75 | 1.38 × 10− 1 | 7.93 | 1.62 | 7.09 × 10− 4 ** |
Polyphen2_HDIV | 5.32 | 0.68 | 7.03 | 0.82 | 2.02 × 10− 1 | 2.30 | 0.33 | 6.22 × 10− 2 | 7.03 | 1.13 | 1.20 × 10− 3 ** |
Polyphen2_HVAR | 4.86 | 0.46 | 5.31 | 0.64 | 1.65 × 10− 1 | 2.07 | 0.21 | 7.22 × 10− 2 | 5.31 | 0.92 | 7.90 × 10− 4 ** |
PROVEAN | 4.33 | 0.66 | 5.23 | 0.86 | 1.04 × 10− 1 | 4.08 | 0.49 | 1.45 × 10− 1 | 5.23 | 1.10 | 4.84 × 10− 4 ** |
SIFT | 5.91 | 0.95 | 7.61 | 1.14 | 1.47 × 10− 1 | 5.43 | 0.64 | 1.16 × 10− 1 | 7.61 | 1.47 | 9.64 × 10− 4 ** |
VEST3 | 3.28 | 0.30 | 4.21 | 0.44 | 1.36 × 10− 1 | 2.24 | 0.17 | 1.13 × 10− 1 | 4.21 | 0.62 | 7.48 × 10− 4 ** |
SKAT-O (all variants) | – | – | 5.41 × 10− 1 | 9.76 × 10− 2 | 3.46 × 10− 2 * | ||||||
SKAT-O (MAF < 0.05) | – | – | 4.63 × 10− 1 | 1.37 × 10− 1 | 5.02 × 10− 2 | ||||||