Overview of Help-Pages

Eldorado: Enhancer Filter

[Introduction] [Filter] [Output] [Sources]


The Enhancer Filter allows to search and filter for Enhancers from various sources (Ensembl, Fantom5, Encode, ...).

The combinable filter categories include:

The result will be displayed in a table which can be sorted and includes links to 'GenomeBrowser', 'More Gene Info' and the 'Enhancer Info'.

Enhancer Filter


Expanding a filter category shows a list of filterable terms along 'badges', that indicate the source this term is found in, and the total count of enhancers this term is associated with.

1. Application

2. Search Filter Terms


The filter result will be displayed in a paged table with (mostly) sortable columns.

Enhancers with any differential expression are highlighted yellow.

1. Columns

Column Description Sortable
Chr - yes
Start Clicking the start position opens the 'GenomeBrowser' at that position. yes
End Clicking the end position opens the 'GenomeBrowser' at that position. yes
Length - yes
Source - yes
#Cell/Tissue Associations

The total number of primary cell, cell line and tissue associations the enhancer has.

Clicking the number of tissue/cell associations opens the 'Enhancer Info' for this enhancer.

Genes The associated genes, including links to 'More Gene Info'. no
Promoter Overlaps The promoters the enhancer is overlapping with. yes

This column gives information about other overlapping enhancers.

An overlap is only counted, if 50% of the smaller enhancer is overlapped by the other.

The overlaps are grouped by their source, and have following format:

<#total overlaps> <Source> (max: <max. overlap percentage for this enhancer>)
16 ENCODE cCREs (max: 4%)
      1 Fantom5 (max: 4%)
yes (sorts by #total overlaps)
Constr. Overlaps

This column shows overlaps with evolutionary constrained elements, omega and pi.

The overlaps are grouped by omega and pi overlaps and have following format:

<Source>: <#overlaps in max. density bin>/<#total overlaps>
omega: 3/18
   pi: 3/13

The max. density bin is calculated by binning the enhancer in 200bp bins and counting the overlaps in every bin.

yes (sorts by #total overlaps in max. density bin)
Specificity Score - yes
Enh. Transcription Score The maximum pooled expression of TCs used to construct each bidirectional loci. yes
Diff. Expression - no
Id - yes

2. Paging


1. Fantom5

Version: Fantom5 phase2.0, reprocessed hg38 v9

Enhancers w/ gene-associations: 22968/52115


2. Ensembl

Version: Release 105, Regulatory build: regulatory features (2021-01-07)

Enhancers w/ gene-associations: 22072/127935



Note: Besides the enhancer-gene-associations from 'Peregrine', this source additionally includes its own enhancer-gene-associations.

Version: Registry V3 (2021)

Enhancers w/ gene-associations: 265952/440504


4. Peregrine

Note: Peregrine data is only used to find enhancer-gene-associations for other source, via overlap.

Version: PANTHER16.0 (2020)