Eldorado: Enhancer Filter

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

Introduction

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

The combinable filter categories include:

Source
Activity
Gene
Cell Line
Primary Cell
Tissue

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

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

Filters can be set/unset by clicking on a term under a filter category.
Clicking a filter, includes the term (blue background), while clicking the '-' icon, excludes it (red background)
The filter is only applied, when the 'Apply Filter' button is clicked. While editing the filter, the currently applied filter will be indicated by a dashed border.
The 'Clear Filter' button, resets the filter, but doesn't apply it.
Inside a filter category terms are 'OR' combined, while different categories are 'AND' combined.
- The 'Activity' filter applies to each of the currently filtered associations (Gene, Cell, Tissue).

2. Search Filter Terms

The filter terms itself can be searched and filtered, by entering the searched term in the text field, under the filter category.

Output

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

Enhancers with any differential expression are highlighted yellow.

1. Columns

Columns can be sorted asc/desc by clicking on the column header.

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

The table controls on the bottom of the table, are used to page through the filter results and change the page size.
The current page can be editted and confirmed by hitting 'enter'.