Chapter 6

The Ensembl Genome Browser: Strategies for Accessing

Eukaryotic Genome Data
Victoria Newman, Benjamin Moore, Helen Sparrow, and Emily Perry

Abstract
The Ensembl Genome Browser provides a wealth of freely available genomic data that can be accessed for
many purposes by genetics, genomics, and molecular biology researchers. Herein we present two protocols
for exploring different aspects of these data: a phenotype and its associated variants and genes, and a pro-
moter and the epigenetic marks and protein-binding activity associated with it. These workflows illustrate
a subset of the data types available through the Ensembl Browser, and can be considered a springboard for
further exploration.

Key words Ensembl, Eukaryotic genomes, Phenotypes, Variants, Epigenetic mark

1 Introduction

Genome browsers are resources that integrate data at the genomic

level, thereby allowing visualization of related genomic informa-
tion in one space. These data can include genes, noncoding ele-
ments that regulate gene expression, genetic variation and the
results of comparative genomics analyses, among other forms of
annotation (Fig. 1) [1–4]. Commonly used genome browsers
include Ensembl, the UCSC Genome Browser [5] and IGV [6].
The Ensembl project was initially launched in 1999 with the aim
of developing methodologies for automatic annotation of (human)
genomic sequence with genes and their constituent transcripts [7].
Since that time, the project has broadened substantially in scope; the
Ensembl Genome Browser [8], which came online in 2000, now
includes reference genomic sequence and annotation for nearly 100
chordate organisms. Ensembl is rapidly incorporating new data,
including whole clades of new species’ genomes and reference
sequence for multiple strains of existing species, such as mouse. In
addition, existing annotation is regularly augmented by the inclu-
sion of new data sets. Ensembl’s sister site, Ensembl Genomes,

Martin Kollmar (ed.), Eukaryotic Genomic Databases: Methods and Protocols, Methods in Molecular Biology, vol. 1757,
https://doi.org/10.1007/978-1-4939-7737-6_6, © The Author(s) 2018

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116 Victoria Newman et al.

Fig. 1 Ensembl features. Ensembl integrates together gene annotation, genetic variation, gene regulation data,
and comparative genomics onto a single genomic platform. Gene annotation is carried out in house, annotating
the full intron–exon structure of coding and noncoding transcripts. Short variants, such as SNPs and indels, are
pulled into Ensembl from external databases, alongside structural variants and copy-number variants. ChIP-­seq
and DNase-seq data is used for in-house prediction of regions of open chromatin and regulatory elements such
as promoters, enhancers and CTCF binding sites on the genome and their activity in different cell types. Whole
genome alignments and gene tree analysis is carried out in house to compare species in Ensembl. These data
are presented alongside each other on the genome in the Ensembl browser, and can also be accessed for bulk
export through BioMart, programmatically through APIs and as flat-files on the Ensembl FTP site

­ rovides access to nonvertebrate genomes through ­dedicated por-

p
tals for Bacteria, Fungi, Plants, Metazoa, and Protists [9, 10].
Ensembl data, annotations, and analyses are updated every
2−3 months, alongside software updates to both the public-facing
website and the underlying databases. Prior releases are frozen as
archive sites, and from Dec 2013 (Ensembl version 74) will remain
accessible via our web interface for at least 5 years following their
initial release. A dedicated site is also maintained for the GRCh37
reference human genome assembly, which is annotated with new
data on a limited basis (Fig. 2) [11]; partial data from ongoing
genome annotation can be accessed via the preview Pre! site.
Data from Ensembl can be accessed at multiple scales. In this
chapter, we describe data access through the browser web pages
and via BioMart [12], a web-based tool that allows customized
retrieval of data from the Ensembl databases. However, data can
also be accessed programmatically via our Perl and REST APIs [13,
14] Files containing genome-wide data are available for all species
represented in Ensembl via an FTP site [15]; data from all releases
 The Ensembl Genome Browsers 117

Fig. 2 The Ensembl homepage. The Ensembl homepage provides access to a search function, which can
retrieve information associated with, for example, genes, transcripts, proteins, variants, phenotypes, and ontol-
ogy terms. In addition, links are available to Ensembl’s sister site, Ensembl Genomes, as well as to the most-­
searched genomes and a complete list of annotated genomes. Fully annotated genomes are available on the
main Ensembl site, while genomes whose annotation is in process can be browsed on the Ensembl Pre! site.
Ensembl maintains web interfaces of archived versions for 5 years. These can be accessed from a link in the
lower right-hand corner. Documentation and help pages can be accessed from the homepage, as well as in-­
house and external tools integrated into the Ensembl web interface. A dedicated page describing data-­
download strategies is also available and presents links to the point-and-click tool BioMart, which permits bulk
download of Ensembl datasets with no requirement for programming expertise, as well as APIs and FTP site

of Ensembl can be retrieved from the FTP site, or from our data-
bases via the Perl APIs, in perpetuity.
Beyond providing access to data related to publicly available
genome annotation, Ensembl integrates a number of tools designed
to process or analyze your own data. The ID History Converter
118 Victoria Newman et al.

converts Ensembl IDs from a previous release into their current

equivalents, while the Assembly Converter maps genomic coordi-
nates from one version of a genome assembly to another. The
Variant Effect Predictor predicts the functional consequences of a
set of known and/or novel variants [16]. Sequence alignment
using BLAST and BLAT against Ensembl genes, genomes and
proteins is also available [17, 18], along with a suite of tools devel-
oped as part of the 1000 Genomes Project [19] that can be accessed
on the dedicated GRCh37 browser site [11].
In this chapter we describe two workflows showcasing a subset
of the data available in the Ensembl browser and indicating possi-
ble routes to access them. First, we demonstrate a phenotype-­
centric search highlighting variation data associated with genes and
transcripts. Secondly, we present a gene-centric search illustrating
gene and transcript models, and the exploration of regulatory fea-
tures in the region of a gene. In each case we also indicate strate-
gies for data export via BioMart. Those interested in our annotation
methods, in programmatic access to Ensembl data, or in exploring
other forms of data and annotation are encouraged to refer to our
publications [20].

2 Materials

Computer, Internet connection.

An Internet browser: recent versions of Firefox, Chrome,
Safari, and Internet Explorer are supported.

3 Methods

These workflows were written using Ensembl release 88 (March

2017). There may be updates to the data or interfaces if you are
using a more recent release.

3.1 WF1: Phenotype-­ The Ensembl browser can be searched using a variety of terms, includ-
Based Searches ing genomic regions, genes, variants, or phenotypes; the following
and Identification workflow describes a phenotype-based search that highlights data and
of Associated Genetic annotations collated in the Phenotype, Variant, Gene, and Transcript
Variation tabs.
Non-melanoma skin cancer—principally basal cell and squa-
mous cell carcinomas—is a relatively common pathology associ-
ated with variants in several genes [21].
1. Getting started: To explore the phenotype in more detail, type
“non-melanoma skin cancer” into the search box on the
Ensembl home page, www.ensembl.org, and click the “Go”
button. The search autocomplete may retrieve direct links to
 The Ensembl Genome Browsers 119

suggested results; this will allow you to proceed immediately

to step 2.
A list of search results will be generated, with “Non-melanoma
skin cancer (Human Phenotype)” appearing first. Options on the
left-hand side of the page permit restriction by species and/or
other categories: click on the different filters individually to apply
them to the search results.
2. Studying loci associated with a phenotype: Click the “Non-­
melanoma skin cancer (Human Phenotype)” link to open the
Phenotype tab.
The loci associated with non-melanoma skin cancer are pre-
sented in tabular form; their external identifiers, genomic coor-
dinates and associated genes, and the publications in which they
were initially described are all listed. Links are provided to fur-
ther information about the annotation source and relevant pub-
lications (in this case, the GWAS catalog [22] and PubMed [23];
Fig. 3).
3. Studying a variant: One of the variants associated with non-­
melanoma skin cancer, rs1805007, falls within the MC1R
gene. Click the “rs1805007” link to load the Variant tab.
The Variant tab collates data relating specifically to the vari-
ant of interest (A full list of the databases from which Ensembl
imports variation data can be found in the documentation
[24].).
An overview of the data is found at the top of the Variant tab
(Fig. 4A), while a table indicating the phenotypes associated with
the variant can be found lower down the page.
The most severe consequence linked to rs1805007 is “missense_
variant”, indicating that the alternative allele at this locus lead
to an amino acid substitution. All consequences of the rs1805007
variant can be explored by clicking on the “See all predicted con-
sequences” link. Ensembl uses Sequence Ontology terms to describe
variant consequences [25].

Fig. 3 The Ensembl phenotype tab. The Ensembl phenotype tab allows you to explore the phenotype ontology
associated with a phenotype and any loci (variants, QTLs, or genes) linked to the phenotype. Loci associated
with the phenotype shown in a table on the Associated loci page. The buttons above the table allow filtering.
Links take you to the database and/or paper where the link between locus and phenotype was made
120 Victoria Newman et al.

Fig. 4 The Ensembl variation tab. The Ensembl variation tab provides a wealth of information about a particular
variant, such as a SNP or indel. (A) A variant summary shown on all pages in the variant tab, including alleles,
MAF, and evidence status. The menu at the left-hand side provides links to all the pages providing information
on the variant. (B) Pie charts from the Population Genetics page, showing the allele frequencies for the variant
in the 1000 Genomes populations. (C) The Genes and Regulation table, listing all genes affected by the variant
with details of sequence ontology consequences, position in the gene and protein, and SIFT and Polyphen
scores for amino acid changes (where relevant)
 The Ensembl Genome Browsers 121

Below the consequence, you can see that the reference allele of
rs1805007 at the genomic position 16:89919709 is C, and one
alternative allele, T, has been observed. Minor allele frequency
(MAF) has been calculated for the alternative allele, which was
observed in 1000 Genomes Project participants: it was identified
in 2% of participants in that study [2, 26].
Navigating to the Variant tab from the Phenotype tab auto-
matically loads a table containing the phenotype data relating to
this variant, as mentioned above. Tanning ability, sensitivity to
sun, and fair hair and skin color have all been associated with the
variant, as has basal cell carcinoma, a form of non-­melanoma
skin cancer. Collectively, these phenotypes are consistent with the
observed linkage between fair complexions and sensitivity to sun
exposure.
4. The menu on the left presents additional options. Click
“Population genetics” to view allele frequencies in global
populations.
On this page, data from the 1000 Genomes [26], HapMap
[27], and NHLBI Exome Sequencing [28] Projects and the
Exome Aggregation Consortium (ExAC) [29] are displayed.
The data from the 1000 Genomes Project are shown at the top
(Fig. 4B); the pie-charts represent allele frequencies for different
superpopulations. Allele frequencies for subpopulations within
each superpopulation can be viewed by clicking the “Sub-­
populations” link beneath the corresponding superpopulation.
Allele and genotype frequencies among 1000 Genomes Project
participants can also be found in tabular form immediately
below the graphical views.
The frequency of the T variant allele in 1000 Genomes Project
participants is highest among European subgroups, and individ-
uals homozygous for the variant also occur only in these subgroups.
This is expected given the phenotypes associated with the variant
(Fig. 4B).
5. To explore genes and transcripts with which the variant is asso-
ciated, click “Genes and regulation” in the menu on the left.
As we saw previously, the variant lies within the MC1R gene;
the summary table here indicates that it overlaps two indepen-
dent transcripts of this gene as a missense variant and is a down-
stream gene variant of a third transcript. Other genes and
transcripts affected by the variant, as well as the associated conse-
quences, are also shown (Fig. 4C).
In a second table, called “Gene expression correlations,” you
can find a list of genes whose expression has been found by the
GTEx Project to be affected by the variant of interest [30].
Finally, any regulatory features or motifs in which the variant
falls will be listed in two separate tables at the bottom of the page.
There are no regulatory features or motifs that overlap the vari-
ant rs1805007.
122 Victoria Newman et al.

6. Studying a gene and its transcripts: Click “ENSG00000258839”

in the Genes and regulation table to go directly to the Gene
tab, which collates gene-related information, for MC1R.
Navigating to the Gene tab from the Variant tab loads the
Variant table, which lists all variants in the Ensembl database
that fall within the gene itself or in the region 5 kb upstream or
downstream of the gene. The top of the page presents a short over-
view of MC1R, including a description of the gene, its genomic
location and synonyms, and an option to show a table of all its
transcripts. This information can also be found at the top of all
subsequent views within the Gene tab. As in other tabs in the
Ensembl browser, the menu to the left of the Gene tab presents
links to a variety of additional data and annotations (Fig. 5A).
7. Click “Summary” in the left-hand menu.
General information about the gene, including a description,
synonyms and the genomic location, can be found in this view. A
graphical model of the gene’s transcripts is shown at the bottom
(Fig. 5A).
8. For the complete set of phenotypes associated with MC1R,
click the “Phenotypes” link in the left-hand menu.
The three tables list phenotypes associated with the gene, with
variants in the gene, and with other species’ orthologues of the
gene, as predicted by the Ensembl comparative genomics pipeline
[3]. Several phenotypes have been linked to rs1805007, and the
MC1R gene also plays a role in coat and skin pigmentation in
other organisms, suggesting a conserved function.
9. Click on the “GO: Biological process” link in the left-hand
menu.
The GO, or Gene Ontology, terms related to biological processes
which have been associated with the transcripts of the MC1R gene
are displayed in the table (Fig. 5B) [31, 32]. Each row of the
table contains the GO accession number, a description of the GO
term, and the evidence codes, annotation source and stable IDs of
transcripts associated with that GO term. Hover over the evidence
codes to see their definitions.
MC1R-encoded proteins are involved in signal transduction
and the melanin biosynthesis pathway, and are located in the
plasma membrane, consistent with a role in pigmentation.

Fig. 5 (continued) against the genome. The central contig indicates the genome. Positive stranded genes, such
as MC1R are depicted above the contig. Strand is also indicated by an arrow alongside the transcript name
indicating the direction of transcription, and by introns, which are shown pointing upward on positive stranded
genes and downward on negative stranded genes. Some transcripts have been removed from this image for
size. On all pages in the gene tab, a menu on the left-hand side lists all the pages available for looking at a
gene. (B) Three pages are available for looking at the GO terms associated with a gene, conforming to the three
categories of terms, Biological process, Molecular function, and Cellular component. These are listed for each
gene, including which transcript they are associated with and how they were annotated
 The Ensembl Genome Browsers 123

Fig. 5 The Ensembl gene tab. The Ensembl gene tab provides a number of views to look at different aspects of
a gene. (A) The gene summary page includes a graphical depiction of the transcripts of the gene, shown
124 Victoria Newman et al.

Two further links in the menu at left provide GO term associa-

tions regarding the Molecular Function and Cellular Component
corresponding to transcripts of the MC1R gene (Fig. 5A).
10. Click on the “External references” link in the left-hand menu.
Links to records in external databases such as EntrezGene
[33], HGNC [34], and MIM Gene and MIM Morbid [35] can
be found on this page.
11. Studying a transcript: Click the “Show transcript table” button
in the “Transcripts” section at the top of the page.
A tabular view of the individual transcripts comprising the
gene model can be seen (for more information on the Ensembl
gene annotation strategy, see ref. 1). This table displays informa-
tion about transcript length and biotype, as well as links to the
entries in the CCDS [36], UniProt [37], and RefSeq [33] data-
bases that correspond to particular transcripts.
The level of support for a transcript prediction, and its biologi-
cal relevance, can be inferred from the matching evidence records
and associated flags.
12. Click the “ENST00000555147.1” link in the Transcript table;
ENST00000555147.1 is the Ensembl stable ID for the MC1R-
001 transcript.
The MC1R-001 transcript’s biotype is listed as “protein-­
coding,” and the transcript is colored golden in the graphical
view. This indicates that it has been independently annotated
with identical coordinates by both the Ensembl automated gene
annotation and the HAVANA manual gene annotation meth-
ods [1] (Fig. 5A).
We are now located in the Transcript tab, which is visible in the
blue navigation bar at the top of the page, next to the Gene tab.
From the left-hand menu of the Transcript tab you can access
complete, spliced or translated transcript sequences (“Exons,”
“cDNA,” and “Protein,” respectively), as well as graphical and
tabular representations of annotated protein domains (“Protein
summary” and “Domains & features,” respectively). “General
identifiers” provides links to related records in external reposito-
ries (Fig. 6A).
You can now click on “Hide Transcript table” in the Gene sec-
tion at the top of the page to remove the Transcript table from the
page view.
13. Click on the “Supporting evidence” link in the left-hand menu.
This page displays the records used in the annotation in graph-
ical form; all records are hyperlinked to the original data in
RefSeq, UniProt, and ENA [38] (Fig. 6B).
14. Click the “Variant table” link in the left-hand menu.
This table displays the set of variants associated with the
MC1R-­001 transcript (Fig. 7A).
 The Ensembl Genome Browsers 125

Fig. 6 The Ensembl transcript tab. The transcript tab contains all views for looking at a transcript and its asso-
ciated protein, where relevant. (A) The left-hand menu on the transcript tab lists all the pages for looking at
transcripts and proteins, and differs subtly from the gene tab menu. It has three different sequence views,
allowing you to view the exon and intron sequences in a table, an alignment of the cDNA, CDS and peptide
sequences, and the protein sequence only. As you open different features, such as genes, transcripts, and
variants, tabs appear in the top bar, allowing easy navigation between the different features you’ve been look-
ing at. (B) The Supporting evidence page shows which cDNA and protein evidence was used to annotate the
transcript model
126 Victoria Newman et al.

15. Filter the table to view missense variants between amino acid
coordinates 150–160.
(a) 
Filter the table for missense variants by clicking
“Consequence” in the Filter section, then “Turn All Off”
and “Missense variant.”
(b) Filter the table to view variants at a specific amino acid
coordinate within the translated sequence of the transcript
by clicking on “Filter Other Columns,” then “AA Coord.”
Use the sliders to restrict the area for which variants are
shown to 150–160.
You can filter this table in numerous ways, including by conse-
quence, source, and genomic or amino-acid coordinates (Fig. 7B).
For missense variants, there are also options to filter by predicted
pathogenicity score, as determined by SIFT [39] and/or PolyPhen
[40] (PolyPhen calculations are available only for human vari-
ants). SIFT and PolyPhen pathogenicity predictions have been
calculated for rs1805007 and the amino acid substitution is con-
sidered deleterious (An additional variant, rs149922657, has
been observed at the same position of MC1R, but has not been
associated with any phenotype.).
16. Click “Haplotypes” in the left-hand menu.
This page allows you to view linked variants that tend to be
coinherited. As a default, the amino acid identities and coordi-
nates of each haplotype are shown, along with their frequencies in
different 1000 Genomes Project populations [26]; however, click-
ing “switch to CDS view” at the top of the table will show nucleo-
tide sequences instead (Fig. 8A). The fifth haplotype listed in the
protein-haplotype table represents our variant of interest. The fre-
quency of this haplotype is, as already seen, higher in the European
subgroup. Lower in the table can be found the 151R>H haplotype
corresponding to rs149922657, the other variant observed at posi-
tion 151; this variant was recovered in only two 1000 Genomes
Project participants.
Clicking on any haplotype will load a table indicating its fre-
quencies in different 1000 Genomes populations in more detail
(Fig. 8B), as well as a sequence view highlighting the nucleotide
and amino-acid positions altered, if applicable (Fig. 8C).
17. Exporting Ensembl variation data: Data can be exported from
Ensembl at multiple scales. A link to the BioMart tool, which
permits the download of customized datasets at intermediate
scale, can be found in the navigation bar at the top of all
Ensembl pages (Fig. 2) [12]. In the BioMart interface, select
the Dataset “Ensembl Variation” (this will also include the
release number, which is 88 at the time of writing), then
“Human Short Variants (SNPs and indels excluding flagged
variants).” To download all variants of ≤50 bp lying within
 The Ensembl Genome Browsers 127

Fig. 7 Table of short variants found within a transcript. The variant table lists all the variants found within a
transcript. A similar page can be found in the gene tab listing all the variants in a gene. The table lists the vari-
ants, which are links to the variant tab, with their positions, alleles, SO consequences, and predicted protein
effects. Buttons above the table allow you to filter to table to only show variants of interest. (A) The unfiltered
table for MC1R-001. (B) The same table, filtered to only show missense variants between residues 150 and
160. The applied filters are shown above the table and can be easily removed
128 Victoria Newman et al.

Fig. 8 Representation of protein haplotypes found in 1000 Genomes individuals. For each of the individuals in
the 1000 Genomes population, the complete protein and CDS sequences were calculated. Sets of cosegregat-
ing variants were defined as protein and transcript haplotypes, their frequencies determined and listed in the
Transcript haplotype page. (A) The table lists all the haplotypes found by the amino acid change. Click on the
haplotype for more details (shown in panels B and C). By default, the page shows the protein haplotypes, but
can be switched to show the CDS haplotypes. (B) The frequency of the selected haplotype across 1000
Genomes subpopulations. (C) An alignment of the reference and haplotype protein and CDS sequences
 The Ensembl Genome Browsers 129

MC1R, as well as 5 kb upstream and downstream of the gene,

filter by “Gene-associated Variant Filters,” selecting “Gene
stable IDs” and inputting “ENSG00000258839,” the stable
ID for the MC1R gene. You can choose attributes of interest
under “Variant” or “Flanking sequences”—for example, the
variant name, source, consequence, start and end coordinates,
and pathogenicity predictions—which will be listed next to
each variant in the output table. Click the “Results” button to
view and download the results table (Fig. 9).

3.2 WF2: Gene-­ The following workflow describes a gene-based search and indicates
Based Searches some of the data and annotations collated in the Gene tab and
and Identification Regulation tab.
of Regulatory Features The POU5F1 gene, formerly known as OCT4, encodes one of
in a Genomic Region the so-called “Yamanaka factors” implicated in cellular de-­
differentiation and induction of pluripotency [41, 42]. We can
search Ensembl to view the POU5F1 gene model and associated
annotation, including predicted regulatory features.
1. Getting started: Type “POU5F1” into the search box on the
homepage, www.ensembl.org, or in the upper right corner of
any browser page, and click “Go.” This will generate a search-­
results page with “POU5F1 (Human Gene)” as the top hit.
Click the title link to navigate directly to the POU5F1 Gene
tab.
The gene “Summary” containing a graphical representation
of the gene model loads by default following navigation from the
search results.
2. Downloading gene sequences: The sequence of the gene and
flanking regions can be downloaded from the Gene tab in two
ways.
(a) To download the sequence in FASTA format for process-
ing in an external tool, simply click the “Export data” but-
ton below the left-hand menu.
This will open a pop-up window that presents customization
options.
(b) To view POU5F1 sequence in the browser, click
“Sequence” in the left-hand menu.
This opens a display in FASTA format; buttons to download
and to BLAST the sequence are shown on this page, and down-
load customization options are similarly available (Fig. 10).
3. Exploring regulatory features: Select “Summary” in the left-­
hand menu. Scroll down to the graphical view of the gene
model and locate the Regulatory Build track.
The Regulatory Build depicts regulatory features that have
been annotated based on epigenome-scale data imported from
sources such as ENCODE [43], Roadmap Epigenomics [44] and
130 Victoria Newman et al.

Fig. 9 The BioMart interface. BioMart allows easy export of tables of gene, variant, or regulatory feature data.
A video tutorial for BioMart is available at https://www.youtube.com/watch?v=QvGT2G0-hYA&ab_channel=E
nsemblHelpdesk

Fig. 10 Exporting gene sequence from Ensembl. All sequence views in Ensembl allow download in either plain
FASTA or annotated rich text format (RTF)
 The Ensembl Genome Browsers 131

Blueprint [45]. These motifs are color-coded according to the pre-

dicted function of the element (Fig. 11A).
4. Click on the red promoter overlapping the 5′ end of the lon-
gest transcript of POU5F1, POU5F1-004, to open a pop-up
box with the stable ID (“ENSR00000195510”), type
(“Promoter”), and genomic coordinates of the core element
and flanking sequences. Click the stable ID to open the
Regulation tab.
Note: POU5F1 is transcribed from the reverse strand, and thus
the 5’ sequences containing the promoter are located to the right of
the gene.
The Regulation tab displays a graphical representation of the
genomic region surrounding the element and a table of the 68 cell
types with regulation data currently in Ensembl, organized by
activity state. In addition to the Regulatory Build, several tracks
are shown by default; these include CRISPR/Cas9 genome-­
editing sites predicted by the Wellcome Trust Sanger Institute
(WTSI) [30], transcription start sites identified by FANTOM5
[46], miRNA binding sites imported from Tarbase [31], and
enhancers identified by VISTA [29]. Tracks with no data in the
immediate region of the feature are not shown (Fig. 11B) (The
term “track” refers to a data type that can be plotted against the
genome.).
Feature activity by cell type can be viewed in graphical form by
clicking the “Select cells” button and, in the resulting pop-up,
choosing “All on” or selecting individual cell types.
5. To view the element’s activation state in individual cell types,
click the “Details by cell type” button at the top of the
Regulation tab or the link in the left-hand menu. Click the
“Select cells” button and then choose “A549” (repressed),
“Placenta” (poised), “Pancreas” (inactive), “GM12878”
(active). Next, click “Select evidence,” then “All on,” to load
the experimental data available for the cell types of interest.
You are now viewing data from cell types in which the element
is active, inactive, poised, and repressed (Fig. 12). These activa-
tion states are determined on the basis of the histone modifications
observed in the region, along with transcription factor and RNA
polymerase II or III binding, as well as areas of DNase I hyper-
sensitivity indicating open chromatin [4].
Additional tracks can be accessed by clicking the “Configure
this page” button, at left, or the cogwheel at the top of the image.
These include the evidence underlying the Regulatory Build, as
well as comparative genomics analyses and variation data that
may provide additional context for the annotated feature.
6. Ensure that both “Peaks” and “Signal” buttons are selected.
Fig. 11 The Ensembl regulatory build and regulatory features. (A) The regulatory build is shown as a track on
the gene image. Clicking on a feature in the track opens a pop-up menu, with a link to the regulatory feature
tab. Some transcripts have been removed from this image for size. (B) The summary page of the regulatory
feature tab contains a table listing activity in different cell types. The graphic shows the feature in context,
along with genes, CRISPR-Cas9 sites and FANTOM5 annotation
 The Ensembl Genome Browsers 133

This will display a summary of the aligned reads (signal) as

well as the peaks for each assay. Annotated features are clickable;
for example, clicking on a predicted promoter will indicate any
transcription factors known to bind it, along with links to the
JASPAR database [47], where further information on motifs is
presented. For other elements, the position of the apex is indicated
with black arrowheads (Fig. 12).
7. To view regulatory features across a larger genomic region,
navigate to the Location tab, available to the left of the Gene
tab in the navigation bar.
The Location tab displays three images: a global view of the
chromosome of interest, an intermediate-scale view providing an
overview of the region flanking the relevant genomic locus (in this
case that of POU5F1), and a final view that presents gene-­
annotation, comparative genomics and variation tracks by
default, along with the Regulatory Build.
It is possible to configure the page to view the activity of local
regulatory features by cell type, along with the evidence underly-
ing these determinations. As in the Regulation tab, tracks depict-
ing other Ensembl annotations can be added to provide context to
the elements shown.
8. Click on the blue “Configure this page” button to add regula-
tory data tracks for the same cell types: A549, placenta, pan-
creas, and GM12878.
This opens a menu listing the many possible tracks available to
display on the genome. Categories of tracks are listed on the left.
Tracks can be turned on and off by clicking on the box alongside
them. To see the activity of regulatory features in different cell
types, turn them on within the “Regulatory features” section. In
the “Histones & polymerases” and “Open chromatin & TFBS”
sections, you will find that tracks are displayed as a matrix, with
cell types along the top and evidence to the side (Fig. 13).
9. Exporting regulatory features with BioMart: A list of regulatory
features, by type, in a genomic region can also be exported via
BioMart. Navigate to BioMart, then select “Ensembl
Regulation” > “Human Regulatory Features” (it may be nec-
essary to refresh the window by clicking “New” if you have
performed a previous query). For features within 5 kb up- and
downstream of POU5F1, filter for Chromosome 6, Base pair
start: 31159337, Base pair end: 31185731. As defaults,
“Chromosome Name,” “Start (bp),” “End (bp),” and
“Feature Type” are selected as Attributes. Add “Regulatory
Stable ID” and generate your results.
Nine features are returned for this genomic region, including
the promoter we explored, ENSR00000195510.
134 Victoria Newman et al.

Fig. 12 Evidence for and activity of regulatory features in different cell types. The Details by cell type page in
the regulatory feature tab can be manipulated to show the activity of the feature in cell types of interest using
the buttons at the top. For each cell type, the feature is shown colour-coded to indicate its activity, with the
evidence shown below. The evidence is ChIP-seq and DNase-seq data, and is shown as peaks of significant
activity and as signal giving the number of reads. The top of the peak is indicated in the peak bar by pairs of
black arrows. Black blocks in the regulatory features indicate the position of transcription factor binding
motifs, which are listed in a pop-up when clicked on
 The Ensembl Genome Browsers 135

Fig. 13 Adding regulation tracks to a region view. The Region in detail view displays a genomic region and can
be customized to show tracks of interest using the Configure this page button. This opens a detailed menu
listing all the available tracks, using categories on the left, including regulatory features and evidence.
Regulatory evidence can be added using a matrix selector, listing the cell type along the top and type of evi-
dence down the left

4 Discussion

Here, we describe methods to navigate variation and regulation

data in the Ensembl browser, focusing on human, although the
principle of navigation is relevant to queries in all species.
The typical entry point to a query in the browser is the search
function. The Ensembl search is versatile and can retrieve informa-
tion linked to a variety of inputs—including, but not limited to,
genomic locations; gene, transcript, protein and regulatory feature
IDs; GO terms; variant IDs; and phenotypes. Unless otherwise
specified in the query, search results for human will be returned
first; filters displayed on the left-hand side of the results page ­permit
the restriction of results by category (e.g., gene, variant) and by
organism.
Selecting a search result will open a tab that collates informa-
tion on the entity: in the two workflows presented above, we pres-
ent strategies for accessing the Phenotype, Variant, Gene,
Transcript, Location, and Regulation tabs following phenotype-
and gene-based searches. As you move from tab to tab in a single
query, previously accessed tabs will remain open in the blue naviga-
tion bar at the top of the page to facilitate seamless data-retrieval in
136 Victoria Newman et al.

a minimal number of steps; you can reenter a previous tab simply

by clicking on the tab header in the navigation bar (Fig. 6A).
By default, tabs will open with a summary of the information
available for each entity (e.g., a transcript or variant), although
herein we indicate a few cases where other data are loaded: for
example, the Gene Variant table is presented immediately upon
navigation from the Variant to the Gene tab. Should a view not be
as expected, links to all data and annotations available in a tab can
be found in the menu on the left; for Location, Gene and Transcript
tabs, these links adhere to a similar framework but present annota-
tions at different scales.
Tabs can be customized by clicking on the blue “Configure
this page” button below the left-hand menu, or the cogwheel icons
that appear in the upper borders of graphical displays (Fig. 13).
Customization allows you to add or remove data tracks that may
be useful to interpretation or analysis; for example, to view the
evidence underlying an activation-state prediction for a regulatory
feature in a cell type of interest (in the Location or Regulation
tabs). Other examples of customization include, in the Location
tab, the addition of tracks containing the data, imported from
external repositories, that were used to annotate transcripts in a
genomic region (ENA, UniProt, and RefSeq tracks accessible in
Location tab) [11]. Public datasets can also be added from the
Track Hub Registry [48], and you can import your own data, in
multiple formats [49], for examination in the context of the
browser.
Data can be exported directly from the browser by clicking the
blue “Export data” buttons found below the left-hand menu in
most tabs, or the “Download sequence” buttons above FASTA
sequences in the Gene and Transcript tabs. In addition, the
BioMart tool described in the workflows presented herein can be
used to retrieve custom datasets from our Gene, Variation and
Regulation databases, and data can be accessed programmatically
from our Perl APIs and REST service. Data from all Ensembl
releases can also be downloaded en masse from our FTP site.
Species’ sequence data and annotations may be updated several
times a year. You should therefore be attentive, when querying
Ensembl data, to the current browser version, as annotations are
subject to change. Data can, however, still be retrieved directly
from archived versions of the browser, as well as via BioMart, while
the browser web interface remains online. Following the decom-
missioning of any browser version, the data remain accessible from
our FTP site and APIs, as mentioned above.
A dedicated email helpdesk is available to field any inquiries
about Ensembl and we typically reply to messages within two days
of receipt. We also hold training workshops upon invitation by
research institutes; from 2013 to 2016 we participated in an aver-
age of 86 workshops, and trained 2150 students, per year. Our
 The Ensembl Genome Browsers 137

training materials are accessible online [50], along with a number

of courses that are available on the Train Online Platform of the
European Bioinformatics Institute (EMBL-EBI) [51], and we
have published a blogpost outlining the process of hosting your
own workshop [52]. Short help videos can be found both on our
YouTube channel [53] and, for those who cannot access YouTube,
on Youku [54]. We invite the community to contact us via help-
desk@ensembl.org for more information about workshops, with
questions regarding the browser, and to suggest features and
resources which would assist their work.

Funding/Acknowledgments

Ensembl receives majority funding from the Wellcome Trust (grant

number WT108749/Z/15/Z) with additional funding for spe-
cific project components from the National Human Genome
Research Institute (U41HG007234 and U41HG007823), the
Biotechnology and Biological Sciences Research Council (BB/
L024225/1, BB/M011615/1, and BB/M020398/1), Open
Targets, the Wellcome Trust (WT104947/Z/14/Z, WT200990/
Z/16/Z, and WT201535/Z/16/Z) and the European Molecular
Biology Laboratory. This project has received funding from the
European Union’s Horizon 2020 research and innovation pro-
gramme under grant agreement n° 634143 (MedBioinformatics).
This project has received funding from the European Union’s
Horizon 2020 research and innovation programme under grant
agreement n° 733161 (MultipleMS).

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