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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%
  1. NA denotes unavailability of the individual score on corresponding region. Glinta denotes conservative results of Glints after excluding CADD, DANN, FATHMM-MKL, MSRV and SinBaD. TOP denotes number of causal variants ranked in top 10, MRR denotes mean rank ratio and AUC denotes area under rank ROC. Some abbreviations for score name: gexp gene expression, gobp gene ontology, kegg KEGG pathway, mrna microRNA regulation, pfam protein families, pseq protein sequence, sign signaling pathway, strg protein-protein interaction, tsfc transcriptional regulation