From: Enhancer variants: evaluating functions in common disease
Reference or method | Input data required | Gene expression | Linear model | Number of genes with predictions (per cell line) | FDR | Species | Publically available |
---|---|---|---|---|---|---|---|
Nearest gene | None | Not considered | Nearest gene | NA | ~40% to 73% | Any | NA |
Nearest expressed gene | Gene expression | Considered | Nearest expressed gene | NA | ~53% to 77% | Any | NA |
Ernst et al.[21] | H3K4me1, H3K4me2, H3K27ac, RNA-seq | Considered | Distance based (125 kb) | NA | Not determined | Human | No |
Thurman et al.[66] | DNase I hypersensitivity | Not considered | Distance based (500 kb) | NA | Not determined | Human | No |
Sheffield et al.[70] | DNase I hypersensitivity and RNA-seq | Considered | 100 kb | NA | Not determined | Human | Predicted interactions: [http://dnase.genome.duke.edu/] |
Shen et al.[67] | H3K4me1, H3K27ac, RNA Pol II | Not considered | Topological domain based | 5,000 to 8,000 | Not determined | Mouse | No |
Andersson et al.[16] | CAGE | Considered | 500 kb | NA | Not determined | Human | No |
PreSTIGE [7] | H3K4me1 | Considered | Distance (100 kb) and CTCF based | 3,000 to 5,000 | ~13% to 23% | Human | Predicted interactions: http://genetics.case.edu/prestige Method application: http://prestige.case.edu |
PreSTIGEouse [68] | H3K4me1 | Considered | Distance based (100 kb) | 3,000 to 5,000 | Not determined | Mouse | Predicted interactions: http://genetics.case.edu/prestige Method application: http://prestige.case.edu |
IM-PET [69] | H3K4me1, H3K27ac, H3K4me3 and RNA-seq* | Considered | Distance (2 Mb) | 7,000 to 10,000 | ~1% | Human | Method application: http://www.healthcare.uiowa.edu/labs/tan/IM-PET.html |