Skip to main content

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

From: GenePy - a score for estimating gene pathogenicity in individuals using next-generation sequencing data

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