Enhancer / Silencer Report
Overview
Each Enhancer / Silencer Report, presented as a web page, has different
blocks of information for Enhancer / Silencer features and the Enhancer /Silencer
sequence. When the curation in these blocks refers to information
that exists on another BKL Report, a hyperlink is
provided that connects to the corresponding BKL Report. For
example, the Enhancer / Silencer Report can include information about the gene
the enhancer / silencer is associated with and provides a link to the
corresponding Locus
Report for that gene.
Please note: Enhancer Reports are only
available for BKL subscribers who have licensed the TRANSFAC
module.
Enhancer / Silencer Reports may be accessed through the Custom Search or through
hyperlinks on BKL reports.
Anatomy of a Enhancer Report
The general structure of a Enhancer / Silencer Report is described
below.
- Access help by clicking the help menu
and clicking the Enhancer report help
link.
- Navigate to the desired section of the report by opening the
table of contents
Points of navigation within the report are indicated by the
following visual cues.
- Links to additional reports within the BKL are presented as
regular text links.
- Links to external resources are indicated by a blue bubble,
such as the PubMedID link shown here:
.
- Links to display additional text within the page are indicated
by a yellow bubble, such as the show abstract link shown
here:
.
- Links providing an option to download content are indicated by
a green bubble, such as the FASTA link shown
here:
.
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Enhancer / Silencer Information |
Provides general information such as genomic coordinates for an enhancer/silencer, the cells/tissues it has been found to be active in
and the genes it supposedly regulates. |
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Genomic coordinates |
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Used genome assembly for the species and the chromosomal location of the enhancer/silencer. |
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Regulated gene(s) |
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Identifies the gene(s) the enhancer/silencer has been found to regulate or be associated with.
The type of experiment that led to the conclusion is given as well. If applicable, the
false discovery rate (FDR) is displayed. The gene
name is hyperlinked to the corresponding Locus Report. |
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Active enhancer in cell(s)/tissue(s) |
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Lists tissues and cell types (or cell lines) the enhancer was found to be active in.
Many enhancers have a narrow tissue specificity, while a few are ubiquitous. |
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Enhancer / Silencer Sequence |
Displays the enhancer/silencer sequence. |
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This block provides a dynamic view of the enhancer/silencer sequence
with its center as the default position. Selected features are displayed above the
sequence - to add or remove features select or deselect the check
box in front of the desired feature. Intervals of species
conservation, as defined by the 46-way phast cons (for human) and
60-way phastcons (for mouse) placental tracks at UCSC, are shown
below the sequence. |
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Features |
Describes the characteristics of a enhancer/silencer. |
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DNase hypersensitivity sites |
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Lists intervals identified by DNase hypersensitivity experiments,
which suggests that the DNA within the interval would be accessible
for binding. The tissue or cell type examined by the experiment is
listed. All data in this table is derived from ENCODE. |
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Histone modifications |
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Identifies DNA fragments shown in vivo to be bound by histones with
a particular modification, based on ChIP-Seq or related
experiments. Cell line/ tissue (and treatment) from which the bound
fragments were derived are included in parentheses. |
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TRANSFAC binding sites |
|
Displays transcription factor binding sites within the enhancer/silencer
sequence. The factor name is hyperlinked to the corresponding Locus
Report and the site accession number to the respective Site Report. |
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ChIP-Seq supported transcription factor binding sites |
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For each ChIP-ChIP or ChIP-Seq experiment for which a matrix
exists, Match was used to predict the most likely region within the
fragment interval that was bound by the factor under investigation.
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SNPs |
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Identifies single nucleotide polymorphisms (SNPs), with hyperlinks
to corresponding dbSNP reports. |
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Identifiers |
Displays internal and external identifiers associated with the enhancer/silencer. |
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BKL Accessions |
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Lists the identifier for the enhancer of the page. |
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External Identifiers |
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Displays identifiers and hyperlinks to corresponding entries of the enhancer/silencer
in external databases, e.g. FANTOM5, HACER, SilencerDB. |
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