Table 2.
Lists of methods for SNP functional priorization.
| Method | Features Used | Classifier |
|---|---|---|
| FunSeq2 [24] | In functional annotations In sensitive regions In ultra-sensitive regions Motif-breaking score (PWM changes) Motif-gaining score (PWM changes) Network centrality score GERP score In ultra-conserved elements In HOT regions In regulatory elements associated with genes Recurrent in multiple samples |
Weighted scoring scheme |
| CADD [123] | conservation metrics; regulatory information; transcript information; protein-level scores (altogether 63 distinct annotations) |
SVM model |
| GWAVA [124] | Open chromatin. Transcription factor binding. Histone modifications. RNA polymerase binding. CpG islands. Genome segmentation. Conservation. Human variation. Genic context. Sequence context. |
Modified random forest algorithm |
| DeepSEA [76] | Evolutionary conservation scores Absolute difference features (919 features) Relative difference features (919 features) |
Boosted logistic regression classifier |
| DeepFind [77] | ~600 DeepBind TF predictor values for the wild type and mutant sequences (altogether ~1,200 features) |
Neural network |