Table 2 The prioritization performance of Glints and individual scores on 1000 Genomes Project based simulated data
From: Global inference of disease-causing single nucleotide variants from exome sequencing data
Method | Exon | Promoter | Intron | Splice site | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
TOP | MRR | AUC | TOP | MRR | AUC | TOP | MRR | AUC | TOP | MRR | AUC | |
CADD | 171 | 12.86% | 87.13% | 0 | 14.66% | 85.33% | 7 | 20.29% | 79.71% | 776 | 13.33% | 87.14% |
DANN | 108 | 10.97% | 89.03% | 0 | 18.99% | 81.02% | 35 | 18.60% | 81.41% | 844 | 9.21% | 91.29% |
FATHMM-MKL | 127 | 11.80% | 88.19% | 0 | 15.20% | 84.80% | 74 | 11.25% | 88.70% | 850 | 8.67% | 91.84% |
Eigen | 95 | 5.47% | 94.50% | 29 | 21.97% | 78.05% | 4 | 14.95% | 85.06% | 218 | 19.89% | 80.52% |
LRT | 0 | 13.17% | 86.95% | NA | NA | NA | NA | NA | NA | NA | NA | NA |
MSRV | 1872 | 7.53% | 92.38% | NA | NA | NA | NA | NA | NA | NA | NA | NA |
MutationAccessor | 583 | 9.81% | 90.16% | NA | NA | NA | NA | NA | NA | NA | NA | NA |
PolyPhen2 | 0 | 8.25% | 91.77% | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SinBaD | 150 | 7.62% | 92.36% | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SIFT | 0 | 13.64% | 86.29% | NA | NA | NA | NA | NA | NA | NA | NA | NA |
GERP | 58 | 16.49% | 83.51% | 2 | 24.29% | 75.70% | 50 | 17.01% | 82.96% | 736 | 12.43% | 88.06% |
Siphy | 60 | 36.37% | 63.63% | 8 | 23.70% | 76.30% | 5 | 47.26% | 52.75% | 391 | 35.16% | 65.06% |
Phylop | 119 | 12.96% | 87.02% | 19 | 26.24% | 73.73% | 79 | 15.87% | 84.06% | 863 | 9.03% | 91.46% |
PhastCons | 0 | 14.12% | 85.78% | 0 | 28.52% | 71.48% | 0 | 15.88% | 84.06% | 585 | 16.22% | 84.21% |
gexp | 1330 | 17.36% | 82.61% | 55 | 21.18% | 78.77% | 101 | 21.25% | 78.74% | 673 | 20.59% | 79.80% |
gobp | 3006 | 10.44% | 89.40% | 56 | 11.47% | 88.33% | 173 | 10.09% | 89.78% | 937 | 11.03% | 89.39% |
kegg | 2321 | 20.21% | 79.85% | 10 | 19.53% | 80.44% | 143 | 20.30% | 79.77% | 737 | 22.16% | 78.34% |
mrna | 1462 | 24.25% | 75.73% | 31 | 30.62% | 69.52% | 96 | 32.99% | 67.05% | 437 | 29.47% | 70.86% |
pfam | 2297 | 17.69% | 82.30% | 53 | 20.93% | 79.13% | 137 | 20.49% | 79.54% | 717 | 20.02% | 80.42% |
pseq | 1194 | 22.21% | 77.87% | 7 | 25.21% | 74.91% | 55 | 23.15% | 76.96% | 697 | 23.78% | 76.70% |
sign | 1447 | 28.10% | 72.07% | 54 | 25.19% | 74.91% | 111 | 32.49% | 67.75% | 507 | 31.01% | 69.49% |
strg | 3086 | 10.96% | 88.92% | 57 | 6.31% | 93.46% | 140 | 11.51% | 88.39% | 922 | 11.28% | 89.17% |
tsfc | 1248 | 30.07% | 69.83% | 37 | 35.64% | 64.28% | 103 | 33.45% | 66.47% | 490 | 33.58% | 66.59% |
Glintsa | 4646 | 2.12% | 97.61% | 82 | 4.51% | 95.26% | 209 | 4.12% | 95.68% | 1012 | 5.20% | 95.29% |
Glints | 4736 | 2.12% | 97.62% | 82 | 3.63% | 96.20% | 219 | 3.65% | 96.13% | 1047 | 4.06% | 96.43% |