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Table 1 Computational approaches to predicting gene targets of enhancer elements

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

  1. *Input data utilized in publication, other input options exist. CAGE, cap analysis of gene expression; CTCF, CCCTC-binding factor (zinc finger protein demonstrated to function as an insulator protein); FDR, false discovery rate; Mb, megabases; NA, not applicable; RNA-seq, RNA sequencing.