| Unsupervised methods |
| Distance | Ranks pairs by inverse linear distance | |
| DNase-DNase | Calculates the Pearson correlation coefficient between the DNase signals at enhancers and promoters across 32 cell-type categories. | [22] |
| DNase-expression | Calculates the Pearson correlation coefficient between the normalized DNase signals at enhancers and normalized gene expression levels measured by microarray across 112 cell types. | [23] |
| GeneHancer | Cell-type agnostic predictions based on co-expression correlations, CHi-C interactions, eQTLs, and genomic distance | [31] |
| Average-rank | Combines the distance and DNase-expression methods by averaging the rank of for each prediction between the two methods | |
| Supervised methods |
| PEP-motif | Features: frequency of motif instances at enhancers and promoters | [28] |
| Classifier: Gradient boosting (XGB package) |
| TargetFinder | Features: Cell-type-specific epigenomic signals (ChIP-seq, DNase, CAGE, etc.) at enhancers, promoters, and the intervening window between enhancers and promoters. | [27] |
| Classifier: Gradient boosting (scikit learn) |
