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Ensembl browser workshop, University of North Carolina at Chapel Hill

Course Details

Lead Trainer
Aleena Mushtaq
Event Dates
2021-11-16 until 2021-11-17
Location
  Virtual
Description
Work with the Ensembl Outreach team to get to grips with the Ensembl browser, accessing and analysing genomic data.
Survey
 Ensembl browser workshop, University of North Carolina at Chapel Hill Course Survey

Demos and exercises

Species and genome assemblies

The front page of Ensembl is found at ensembl.org. It contains lots of information and links to help you navigate Ensembl:

At the top left you can see the current release number and what has come out in this release. To access old releases, scroll to the bottom of the page and click on View in archive site.

Click on the links to go to the archives. Alternatively, you can jump quickly to the correct release by putting it into the URL, for example e98.ensembl.org jumps to release 98.

Click on View full list of all species.

Click on the common name of your species of interest to go to the species homepage. We’ll click on Human.

Here you can see links to example pages and to download flatfiles. To find out more about the genome assembly and genebuild, click on More information and statistics.

Here you’ll find a detailed description of how to the genome was produced and links to the original source. You will also see details of how the genes were annotated.

The current genome assembly for human is GRCh38. If you want to see the previous assembly, GRCh37, visit our dedicated site grch37.ensembl.org.

Let’s take a look at the Ensembl Genomes homepage at ensemblgenomes.org.

Click on the different taxa to see their homepages. Each one is colour-coded.

You can navigate most of the taxa in the same way as you would with Ensembl, but Ensembl Bacteria has a large number of genomes, so needs slightly different methods. Let’s look at it in more detail.

There’s no full species list for bacteria as it would be hard to navigate with the number of species. To find a species, start to type the species name into the species search box. A drop down list will appear with possible species.

For example, to find a sub-strain of Clostridioides difficile start typing in the species name. Due to the autocomplete, you’ll see useful results as soon as you get to clostridio.

The drop down contains various strains of Clostridioides difficile. Let’s choose Clostridioides difficile 630. This will take us to another species homepage, where we can explore various features.

Unlike the human homepage, there is no prose description of the genome or gene annotation, as these pages were generated automatically.

Our newest genomes, such as those coming from the Darwin Tree of Life, are available rapid.ensembl.org with limited annotation.

Panda species data

(a) Go to the species homepage for Panda. What is the name of the genome assembly for Panda?

(b) Click on More information and statistics. How long is the Panda genome (in bp)? How many genes have been annotated?

(a) Select Panda from the drop down species list, or click on View full list of all Ensembl species, then choose Panda from the list.

The assembly is ASM200744v2 or GCA_002007445.2.

(b) Click on More information and statistics. Statistics are shown in the tables on the left.

The length of the genome is 2,444,060,653 bp.
There are 20,857 coding genes.

Available zebrafish assemblies

What previous assemblies are available for zebrafish?

Click on Zebrafish on the front page of Ensembl to go to the species homepage. Under Other assemblies three previous assembly names and the releases you can find them in are listed.

Assembly GRCz10 is available in the archived release 91, Zv9 in 79 and Zv8 in 54.

Mosquito species

(a) Go to Ensembl Metazoa. How many species of the genus Anopheles are there in Ensembl Metazoa?

(b) When was the current Anopheles gambiae genome assembly last revised?

(a) Go to metazoa.ensembl.org. Open the drop down list or click on View full list of all Ensembl Metazoa species. In a latin binomial species name, the first word represents the genus. Type Anopheles into the filter box in the top left to find all genomes with this word in the binomial.

There are 22 Anopheles species.

(b) Click on Anopheles gambiae, then on More information and statistics.

The genome was revised in February 2006.

Finding genomes with species search on Ensembl Bacteria

Mycobacterium tuberculosis H37Ra str. ATCC25177 is a clinical strain.

Go to Ensembl Bacteria and find the species Mycobacterium tuberculosis H37Ra str. ATCC25177 (Hint: type H37Ra into the Search for a genome box). How many coding genes does it have?

Go to bacteria.ensembl.org and start to type the name H37Ra into the search species box. It will autocomplete, allowing you to select Mycobacterium tuberculosis H37Ra str. ATCC25177 from the drop-down list. Click on More information and statistics.

Mycobacterium tuberculosis H37Ra str. ATCC25177 has 4034 coding genes and 48 non-coding.

Exploring genomic regions

Start at the Ensembl front page, ensembl.org. You can search for a region by typing it into a search box, but you have to specify the species.

To bypass the text search, you need to input your region coordinates in the correct format, which is chromosome, colon, start coordinate, dash, end coordinate, with no spaces for example: human 4:122868000-122946000. Type (or copy and paste) these coordinates into either search box.

or

Press Enter or click Go to jump directly to the Region in detail Page.

Click on the button to view page-specific help. The help pages provide text, labelled images and, in some cases, help videos to describe what you can see on the page and how to interact with it.

The Region in detail page is made up of three images, let’s look at each one in detail.

  1. The first image shows the chromosome:

The region we’re looking at is highlighted on the chromosome. You can jump to a different region by dragging out a box in this image. Drag out a box on the chromosome, a pop-up menu will appear.

If you wanted to move to the region, you could click on Jump to region (### bp). If you wanted to highlight it, click on Mark region (###bp). For now, we’ll close the pop-up by clicking on the X on the corner.

  1. The second image shows a 1Mb region around our selected region. This is always 1Mb in human, but the fixed size of this view varies between species. This view allows you to scroll back and forth along the chromosome.

You can also drag out and jump to or mark a region.

Click on the X to close the pop-up menu.

Click on the Drag/Select button to change the action of your mouse click. Now you can scroll along the chromosome by clicking and dragging within the image. As you do this you’ll see the image below grey out and two blue buttons appear. Clicking on Update this image would jump the lower image to the region central to the scrollable image. We want to go back to where we started, so we’ll click on Reset scrollable image.

  1. The third image is a detailed, configurable view of the region.

Here you can see various tracks, which is what we call a data type that you can plot against the genome. Some tracks, such as the transcripts, can be on the forward or reverse strand. Forward stranded features are shown above the blue contig track that runs across the middle of the image, with reverse stranded features below the contig. Other tracks, such as variants, regulatory features or conserved regions, refer to both strands of the genome, and these are shown by default at the very top or very bottom of the view.

You can use click and drag to either navigate around the region or highlight regions of interest, Click on the Drag/Select option at the top or bottom right to switch mouse action. On Drag, you can click and drag left or right to move along the genome, the page will reload when you drop the mouse button. On Select you can drag out a box to highlight or zoom in on a region of interest.

With the tool set to Select, drag out a box around an exon and choose Mark region.

The highlight will remain in place if you zoom in and out or move around the region. This allows you to keep track of regions or features of interest.

We can edit what we see on this page by clicking on the blue Configure this page menu at the left.

This will open a menu that allows you to change the image.

There are thousands of possible tracks that you can add. When you launch the view, you will see all the tracks that are currently turned on with their names on the left and an info icon on the right, which you can click on to expand the description of the track. Turn them on or off, or change the track style by clicking on the box next to the name. More details about the different track styles are in this FAQ: http://www.ensembl.org/Help/Faq?id=335.

You can find more tracks to add by either exploring the categories on the left, or using the Find a track option at the top left. Type in a word or phrase to find tracks with it in the track name or description.

Let’s add some tracks to this image. Add:

  • Proteins (mammal) from UniProt – Labels
  • 1000 Genomes - All - short variants (SNPs and indels) – Normal

Now click on the tick in the top left hand to save and close the menu. Alternatively, click anywhere outside of the menu. We can now see the tracks in the image. The proteins track is stranded, so you will see two tracks, one above and one below the contig, representing the proteins mapped to the forward and reverse strands respectively. The variants track is not stranded, so is found near the bottom of the image.

If the track is not giving you can information you need, you can easily change the way the tracks appear by hovering over the track name then the cog wheel to open a menu. To make it easier to compare information between tracks, such as spotting overlaps, you can move tracks around by clicking and dragging on the bar to the left of the track name.

Now that you’ve got the view how you want it, you might like to show something you’ve found to a colleague or collaborator. Click on the Share this page button to generate a link. Email the link to someone else, so that they can see the same view as you, including all the tracks you’ve added. These links contain the Ensembl release number, so if a new release or even assembly comes out, your link will just take you to the archive site for the release it was made on.

To return this to the default view, go to Configure this page and select Reset configuration at the bottom of the menu.

Exploring a genomic region in human

(a) Go to the region from 31,937,000 to 32,633,000 bp on human chromosome 13. On which cytogenetic band is this region located? How many contigs make up this portion of the assembly (contigs are contiguous stretches of DNA sequence that have been assembled solely based on direct sequencing information)?

(b) Zoom in on the BRCA2 gene.

(c) Configure this page to turn on the LTR (repeat) track in this view. What tool was used to annotate the LTRs according to the track information? How many LTRs can you see within the BRCA2 gene? Do any overlap exons?

(d) Create a Share link for this display. Email it to your neighbour. Open the link they sent you and compare. If there are differences, can you work out why?

(e) Export the genomic sequence of the region you are looking at in FASTA format.

(f) Turn off all tracks you added to the Region in detail page.

(a) Go to the Ensembl homepage.

Select Search: Human and type 13:31937000-32633000 in the text box (or alternatively leave the Search drop-down list like it is and type human 13:31937000-32633000 in the text box). Click Go.

This genomic region is located on cytogenetic band q13.1. It is made up of eight contigs, indicated by the alternating light and dark blue coloured bars in the Contigs track. Note that KF455761.1 is a tiny contig that splits AL137143.8 in two.

(b) Draw with your mouse a box encompassing the BRCA2 transcripts. Click on Jump to region in the pop-up menu.

(c) Click Configure this page in the side menu (or on the cog wheel icon in the top left hand side of the bottom image).

Go into Repeats in the left-hand menu then select LTR. Click on the (i) button to find out more

Repeat Masker was used to annotate LTRs onto the genome.

Save and close the new configuration by clicking on ✓ (or anywhere outside the pop-up window).

There are seven LTRs overlapping BRCA2, none of them overlap exons.

(d) Click Share this page in the side menu. Select the link and copy. Get your neighbour’s email address and compose an email to them, paste the link in and send the message.

When you receive the link from them, open the email and click on your link. You should be able to view the page with the new configuration and data tracks they have added to in the Location tab. You might see differences where they specified a slightly different region to you, or where they have added different tracks.

Here is the Share link from the video answer: http://may2021.archive.ensembl.org/Homo_sapiens/Share/71a173bba78f0dbe03e48d3240424943?redirect=no;mobileredirect=no

(e) Click Export data in the side menu. Leave the default parameters as they are (FASTA sequence should already be selected). Click Next>. Click on Text.

Note that the sequence has a header that provides information about the genome assembly (GRCh38), the chromosome, the start and end coordinates and the strand. For example:

>13 dna:chromosome chromosome:GRCh38:13:32311910:32405865:1

(f) Click Configure this page in the side menu. Click Reset configuration. Click ✓.

Exploring CRISPR sites in a human genomic region

You want to do some CRISPR manipulation of the human SMC3 gene. You’re looking for a CRISPR editing site within the locus 10:110578600-110578700.

(a) Go to the locus above and turn on the CRISPR track. How many CRISPR sites can you see in this locus?

(b) Do any of the CRISPR sites overlap any phenotype causing variants? What are the identifiers of these sites and variants?

(c) Mark the region of the negative strand CRISPR site that overlaps these variants, then zoom out to see the whole SMC3 gene. What exon number is your CRISPR site found in the SMC3-201 transcript?

(a) Go to the Ensembl homepage.

Select Search: Human and type 10:110578600-110578700 in the text box (or alternatively leave the Search drop-down list like it is and type human 10:110578600-110578700 in the text box). Click Go.

Click Configure this page. Type crispr in the Find a track text box. Select CRISPR Cas9 in Labels.

There are five positive strand and three negative strand CRISPR sites.

(b) Click on the variants and CRISPR sites to get their identifiers.

1074131234, 1074131235 and 1074131236 overlap rs113411202 and rs1064797151. 1074131234 and 1074131235 overlap rs779773957. 1074131234 and 1074131235 also overlap rs779773957

(c) Click and drag a box around the site, then select Mark region. In the overview above, click and drag a box around the SMC3 gene then select Jump to region. Count the exons to get the number where the marked region is found.

The site is found in exon 7.

Exploring assembly exceptions in human

(a) Go to the region 21:32630000-32870000 in human. What is the red highlighted region? What is its name?

(b) Can you see the assembly exceptions in the chromosome overview at the top? How many regions with assembly exceptions are there on chromosome 21?

(c) Can you compare this assembly exception with the reference? What is different between this assembly exception and the version on the primary assembly?

(a) Go to the Ensembl homepage.

Select Search: Human and type 21:32630000-32870000 in the text box (or alternatively leave the Search drop-down list like it is and type human 21:32630000-32870000 in the text box). Click Go.

You will see a red highlighted region in the middle of this region. Click on the thin dark red bar in any of the three views to see the label _CHR_HSCHR21_3_CTG1_1:32769079-32843731__. Click on _What are assembly exceptions? to open a new window which explains assembly exceptions.

(b) Assembly exceptions are marked in the chromosome view at the top.

There are seven haplotypes on chromosome 21 and one patch.

(c) Another option in the drop-down is Compare with reference. Click on this.

Scroll down the page to see the comparison between the haplotype and primary assembly. Aligned sequences are highlighted in pink and linked together in green.

The assembly exception CHR_HSCHR21_3_CTG1_1 contains an extra region compared to the primary assembly.

Exploring a genomic region in rice

(a) Go to the region 1:405000-453000 in Oryza sativa Japonica.

(b) Turn on the AGILENT:G2519F-015241 microarray track. Are there any oligo probes that map to this region?

(c) Highlight the region around any reverse strand probes you can see. Do they map to any transcripts?

(a) Go to the Ensembl Plants homepage.

Select Search: Oryza sativa Japonica and type 1:405000-453000. Click Go.

(b) Click on Configure this page to open the menu. You can find the AGILENT:G2519F-015241 track under Oligo probes in the left hand menu, or by using the Find a track box at the top right. Turn on the track then save and close the menu.

As the AGILENT:G2519F-015241 track is stranded, it appears at the top and bottom of the view, in green.

There are five probes mapped to this region on the positive strand and one probe on the reverse strand.

(c) Drag a box around the reverse strand probe then click on Mark region to highlight.

The highlighted region maps to two transcripts: Os01t0107900-02 and Os01t0107900-01

Exploring a genomic region in Salmonella enterica

(a) Search for the Salmonella enterica subsp. enterica serovar Typhi str. Ty2 (Hint: type Ty2 into the Search for a genome box).

(b) Go to the region Chromosome:2000605-2009742.

(c) How many genes are annotated in this region? How many are on the forward strand? How many are on the reverse strand?

(a) Go to the Ensembl Bacteria homepage.

Type Ty2 into the Search for a Genome box. Click on the auto-completed genome name to navigate to the species homepage.

(b) Type Chromosome:2000605-2009742 into the search box. Click Go.

(c)

There are eight genes annotated in this region, all on the reverse strand.

Genes and transcripts

You can find out lots of information about Ensembl genes and transcripts using the browser. If you’re already looking at a region view, you can click on any transcript and a pop-up menu will appear, allowing you to jump directly to that gene or transcript.

Alternatively, you can find a gene by searching for it. You can search for gene names or identifiers, and also phenotypes or functions that might be associated with the genes.

We’re going to look at the human UQCRQ gene. From ensembl.org, type UQCRQ into the search bar and click the Go button. You will get a list of hits with the human gene at the top.

Where you search for something without specifying the species, or where the ID is not restricted to a single species, the most popular species will appear first, in this case, human, mouse and zebrafish appear first. You can restrict your query to species or features of interest using the options on the left.

The gene tab

Click on the gene name or Ensembl ID. The Gene tab should open:

This page summarises the gene, including its location, name and equivalents in other databases. At the bottom of the page, a graphic shows a region view with the transcripts. We can see exons shown as blocks with introns as lines linking them together. Coding exons are filled, whereas non-coding exons are empty. We can also see the overlapping and neighbouring genes and other genomic features.

There are different tabs for different types of features, such as genes, transcripts or variants. These appear side-by-side across the blue bar, allowing you to jump back and forth between features of interest. Each tab has its own navigation column down the left hand side of the page, listing all the things you can see for this feature.

Let’s walk through this menu for the gene tab. How can we view the genomic sequence? Click Sequence at the left of the page.

The sequence is shown in FASTA format. The FASTA header contains the genome assembly, chromosome, coordinates and strand (1 or -1) – this gene is on the positive strand.

Exons are highlighted within the genomic sequence, both exons of our gene of interest and any neighbouring or overlapping gene. By default, 600 bases are shown up and downstream of the gene. We can make changes to how this sequence appears with the blue Configure this page button found at the left. This allows us to change the flanking regions, add variants, add line numbering and more. Click on it now.

Once you have selected changes (in this example, Show variants, 1000 Genomes variants and Line numbering) click at the top right.

You can download this sequence by clicking in the Download sequence button above the sequence:

This will open a dialogue box that allows you to pick between plain FASTA sequence, or sequence in RTF, which includes all the coloured annotations and can be opened in a word processor. If you want run a sequence analysis tool, download as FASTA sequence, whereas if you want to analyse the sequence visually, RTF is best for this. This button is available for all sequence views.

To find out what the protein does, have a look at GO terms from the Gene Ontology consortium. There are three pages of GO terms, representing the three divisions in GO: Biological process (what the protein does), Cellular component (where the protein is) and Molecular function (how it does it). Click on GO: Biological process to see an example of the GO pages.

Here you can see the functions that have been associated with the gene. There are three-letter codes that indicate how the association was made, as well as links to the specific transcript they are linked to.

We also have links out to other databases which have information about our genes and may focus on other topics that we don’t cover, like Gene Expression Atlas or OMIM. Go up the left-hand menu to External references:

Demo: The transcript tab

We’re now going to explore the different transcripts of UQCRQ. Click on Show transcript table at the top.

Here we can see a list of all the transcripts of UQCRQ with their identifiers, lengths, biotypes and flags to help you decide which ones to look at.

If we were to only choose one transcript to analyse, we would choose UQCRQ-203 because it is the MANE Select and Ensembl Canonical. This means it is both 100% identical to the RefSeq transcript NM_014402.5 and both Ensembl and NCBI agree that it is the most biologically important transcript.

Click on the ID, ENST00000378670.8.

You are now in the Transcript tab for UQCRQ-203. We can still see the gene tab so we can easily jump back. The left hand navigation column provides several options for the transcript UQCRQ-203 - many of these are similar to the options you see in the gene tab, but not all of them. If you can’t find the thing you’re looking for, often the solution is to switch tabs.

Click on the Exons link. This page is useful for designing RT-PCR primers because you can see the sequences of the different exons and their lengths.

You may want to change the display (for example, to show more flanking sequence, or to show full introns). In order to do so click on Configure this page and change the display options accordingly.

Now click on the cDNA link to see the spliced transcript sequence with the amino acid sequence. This page is useful for mapping between the RNA and protein sequences, particularly genetic variants.

UnTranslated Regions (UTRs) are highlighted in dark yellow, codons are highlighted in light yellow, and exon sequence is shown in black or blue letters to show exon divides. Sequence variants are represented by highlighted nucleotides and clickable IUPAC codes are above the sequence.

Next, follow the General identifiers link at the left. Just like the External References page in the gene tab, this page shows links out to other databases such as RefSeq, UniProtKB, PDBe and others, this time linked to the transcript or protein product, rather than the gene.

If you’re interested in protein domains, you could click on Protein summary to view domains from Pfam, PROSITE, Superfamily, InterPro, and more. These are all plotted against the transcript sequence, with the exons shown in alternating shades of purple at the top of the page. Alternatively, you can go to Domains & features to see a table of the same information.

You can also see the structure of the protein from the PDB by clicking on 3D Protein model.

This uses LiteMol to show a 3D protein. You can use all the normal controls that you would use with LiteMol, plus plot Ensembl features like Exons and variants onto the structure using the options on the right. We allow you to see the top ten PDB models for this protein, based on coverage and quality scores, you can choose which at the top of the viewer.

Exploring the human MYH9 gene

(a) Find the human MYH9 (myosin, heavy chain 9, non-muscle) gene, and go to the Gene tab.

  • On which chromosome and which strand of the genome is this gene located?
  • How many transcripts (splice variants) are there and how many are protein coding?
  • What is the longest transcript, and how long is the protein it encodes?
  • Which transcript would you take forward for further study?

(b) Click on Phenotypes at the left side of the page. Are there any diseases associated with this gene, according to MIM (Mendelian Inheritance in Man)?

(c) What are some functions of MYH9 according to the Gene Ontology consortium? Have a look at the GO pages for this gene.

(d) In the transcript table, click on the transcript ID for MYH9-201, and go to the Transcript tab.

  • How many exons does it have?
  • Are any of the exons completely or partially untranslated?
  • Is there an associated sequence in UniProtKB/Swiss-Prot? Have a look at the General identifiers for this transcript.

(e) Are there microarray (oligo) probes that can be used to monitor ENST00000216181 expression?

(a) Go to the Ensembl homepage (http://www.ensembl.org).

Select Search: Human and type MYH9. Click Go.

Click on either the Ensembl ID ENSG00000100345 or the HGNC official gene name MYH9.

  • Chromosome 22 on the reverse strand.
  • Ensembl has 11 transcripts annotated for this gene, of which three are protein coding.
  • The longest transcript is MYH9-201 and it codes for a protein of 1,960 amino acids
  • MYH9-201 is the transcript I would take forward for further study, as it is the MANE Select.

(b) Click on Phenotypes at the left to see the associated phenotypes. There is a large table of phenotypes. To see only the ones from MIM, type mim into the filter box at the top right of the table.

These are some of the phenotypes associated with MYH9 according to MIM: autosomal dominant deafness and Macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss. Click on the records for more information.

(c) > The Gene Ontology project (http://www.geneontology.org/) maps terms to a protein in three classes: biological process, cellular component, and molecular function. Meiotic spindle organisation, cell morphogenesis, and cytokinesis are some of the roles associated with MYH9.

(d) Click on ENST00000216181.11

  • It has 41 exons, shown in the Transcript summary.

Click on the Exons link in this side menu.

  • Exon 1 is completely untranslated, and exons 2 and 41 are partially untranslated (UTR sequence is shown in orange). You can also see this in the cDNA view if you click on the cDNA link in the left side menu.
  • P35579-1 from UniProt/Swiss-Prot matches the translation of the Ensembl transcript. Click on P35579-1 to go to UniProtKB, or click align for the alignment.

(e) Click on Oligo probes in the side menu.

Probesets from Affymetrix, Agilent, Codelink, Illumina, and Phalanx match to this transcript sequence. Expression analysis with any of these probesets would reveal information about the transcript. Hint: this information can sometimes be found in the ArrayExpress Atlas: www.ebi.ac.uk/arrayexpress/

Finding a gene associated with a phenotype

Phenylketonuria is a genetic disorder caused by an inability to metabolise phenylalanine in any body tissue. This results in an accumulation of phenylalanine causing seizures and mental retardation.

(a) Search for phenylketonuria from the Ensembl homepage and narrow down your search to only genes. What gene is associated with this disorder?

(b) How many protein coding transcripts does this gene have? View all of these in the transcript comparison view.

(c) What is the MIM gene identifier for this gene?

(d) Go to the MANE Select transcript and look at its 3D structure. In the model 2pah, how many protein molecules can you see?

(a) Start at the Ensembl homepage (http://www.ensembl.org).

Type phenylketonuria into the search box then click Go. Choose Gene from the left hand menu.

The gene associated with this disorder is PAH, phenylalanine hydroxylase, ENSG00000171759.

(b) If the transcript table is hidden, click on Show transcript table to see it.

There are six protein coding transcripts.

Click on Transcript comparison in the left hand menu. Click on Select transcripts. Either select all the transcripts labelled protein coding one-by-one, or click on the drop down and select Protein coding. Close the menu.

(c) Click on External references.

The MIM gene ID is 612349.

(d) Open the transcript table and click on the ID for the MANE Select: ENST00000553106.6. Go to 3D protein model in the left-hand menu.

The model 2pah is shown by default. It has two protein molecules in it. You may need to rotate the model to see this clearly.

Exploring the mouse Dpp6 gene

Genetic variation in the dipeptidylpeptidase 6 Gene (DPP6) in humans has previously been strongly associated with amyotrophic lateral sclerosis (ALS), a lethal disorder caused by progressive degeneration of motor neurons in the brain.

(a) Search for the Dpp6 gene in mouse and click on the ENSMUST00000071500 transcript to open the transcript tab. How many exons make up this transcript?

(b) Click on Exons to display the exon sequences of the transcript. Which exon contains the translation start? What is the exon ID of the largest exon? What is the start and end phase of exon 2?

(c) Click on Protein summary. How many protein domains or features fall within the second exon? What is the PFAM protein domain at the C-terminus of the protein and how many exons does it fall into? Which amino acid positions does the domain above cover?

(d) Click on Domains and features. Which domains are associated with Pfam? How many genes in the mouse genome have the IPR002469 domain? What chromosomes are these genes found on?

(a) Go to the Ensembl homepage.

Select Search: Mouse and type Dpp6. Click Go.

Click on either the Ensembl ID ENSMUSG00000061576 or the MGI official gene name Dpp6. From the transcript table, click on the link for transcript ENSMUST00000071500 to open the transcript tab.

ENSMUST00000071500 consists of 26 exons.

(b) Click on Exons, which can be found on the left of the page. The translation start is found in the first exon (ENSMUSE00000725552), shown in dark blue text.

The largest exon is the final exon (856 bp), which has the exon ID ENSMUSE00000773588.

Exon 2 has a start and end phase of 0 and 1 respectively, which means that the codon at the start of the exon starts at the first nucleotide and the codon at the end of the exon ends at nucleotide 2. Notice that the end phase of each exon is the same as the start phase of the next exon.

(c) Click on Protein Summary in the menu on the left hand side of the page. Alternating exons are shown on the protein as different shades of purple.

There are two predicted protein domains that fall within the second exon: low complexity (seg) and a transmembrane helix.

Click on a domain or feature to view further information.

The C-terminal PFAM domain is Peptidase_S9B (PF00326), which spans or partially spans seven exons, covering amino acid positions 582-787.

(d) Click on Domains & features.

Looking at the Domains table you should notice that there are two domains associated with Pfam: PF00326 and PF00930.

Click on Display all genes with this domain next to IPR002469. This should now display the genes that have the IPR002469 domain located on the karyotype and as a table.

Six genes have this domain and they are found on chromosomes 1, 2, 5, 9 and 17.

Exploring a plant gene (Vitis vinifera, grape)

Start in http://plants.ensembl.org/index.html and select the Vitis vinifera genome.

(a) What GO: biological process terms are associated with the MADS4 gene?

(b) Go to the transcript tab for the only transcript, Vv01s0010g03900.t01. How many exons does it have? Which one is the longest? How much of that is coding?

(c) What domains can be found in the protein product of this transcript? How many different domain prediction methods agree with each of these domains?

(a) Go to http://plants.ensembl.org/index.html.

Select Vitis vinifera from the drop down menu All genomes – select a species or click on View full list of all Ensembl Plants species and then choose V. vinifera.

Type MADS4 and click on the gene link VIT_01s0010g03900. Click on GO: Biological process in the side menu.

There are seven terms listed including GO:0006351, transcription, DNA-templated, and GO:0006355, regulation of transcription, DNA-templated.

(b) Click on the transcript named Vv01s0010g03900.t01 (or on the Transcript tab). Click on Exons in the left hand menu.

There are eight exons. Exon 8 is longest with 303 bp, of which 13 are coding.

(c) Click on either Protein Summary or Domains & features in the left hand menu to see graphically or as a table respectively.

A MADS-box domain near the N-terminus is identified by eight domain prediction methods. A K-box domain near the C-terminus is identified by two. Two coiled-coils are identified by one.

Variation

In any of the sequence views shown in the Gene and Transcript tabs, you can view variants on the sequence. You can do this by clicking on Configure this page from any of these views.

Let’s take a look at the Gene sequence view for HBB in human. Search for HBB and go to the Sequence view.

If you can’t see variants marked on this view, click on Configure this page and select Show variants: Yes and show links. You may also wish to add a filter to the variants to allow them to load more quickly, we’ll add Filter variants by evidence status: 1000Genomes.

Find out more about a variant by clicking on it.

You can add variants to all other sequence views in the same way.

You can go to the Variation tab by clicking on the variant ID. For now, we’ll explore more ways of finding variants.

To view all the sequence variants in table form, click the Variant table link at the left of the gene tab.

You can filter the table to only show the variants you’re interested in. For example, click on Consequences: All, then select the variant consequences you’re interested in. For display purposes, the table above has already been filtered to only show missense variants.

You can also filter by the different pathogenicity scores and MAF, or click on Filter other columns for filtering by other columns such as Evidence or Class.

The table contains lots of information about the variants. You can click on the IDs here to go to the Variation tab too.

You can also see the phenotypes associated with a gene. Click on Phenotype in the left hand menu.

Open the transcript table and go to HBB-201 ENST00000335295, then click on Haplotypes in the left hand menu.

The Haplotypes view in the transcript tab shows you the actual protein and CDS sequences in 1000 Genomes individuals. This is possible because the 1000 Genomes study has phased genotypes, so we know which alleles occur on which of the chromosome pairs. The table lists all the versions of the protein that occur along with their frequencies, including the reference sequence and sequences with one or more alternative alleles.

Click on one of the haplotypes, we’ll go for 18K>*,​19del{130}, to find out more about it. Here you will see the frequency in the 1000 Genomes subpopulations, the sequence and the 1000 Genomes individuals where this protein is found.

Let’s have a look at variants in the Location tab. Click on the Location tab in the top bar.

Configure this page and open Variation from the left-hand menu.

There are various options for turning on variants. You can turn on variants by source, by frequency, presence of a phenotype or by individual genome they were isolated from. You can also turn on genotyping chips.

Let’s have a look at a specific variant. If we zoomed in we could see the variant rs334 in this region, however it’s easier to find if we put rs334 into the search box. Click through to open the Variation tab.

The icons show you what information is available for this variant. Click on Genes and regulation, or follow the link on the left.

This page illustrates the genes the variant falls within and the consequences on those genes, including pathogenicity predictors. It also shows data from GTEx on genes that have increased/decreased expression in individuals with this variant, in different tissues. Finally, regulatory features and motifs that the variant falls within are shown.

We can also see the variant in the protein structure by clicking on 3D Protein model.

This is a LiteMol viewer, where you can rotate and zoom in on the structure. The variant location is highlighted, so you can see where it lands within the structure.

Let’s look at population genetics. Click on Population genetics in the left-hand menu.

The population allele frequencies are shown by study, including 1000 Genomes and gnomAD. Where genotype frequencies are available, these are shown in the tables.

There are big differences in allele frequencies between populations. Let’s have a look at the phenotypes associated with this variant to see if they are known to be specific to certain human populations. Click on Phenotype Data in the left-hand menu.

This variant is associated with various phenotypes, including sickle cell and malaria resistance. These phenotype associations come from sources including the GWAS catalog, ClinVar, Orphanet and OMIM. Where available, there are links to the original paper that made the association, the allele that is associated with the phenotype and p-values and other statistics.

Human population genetics and phenotype data

The SNP rs1738074 in the 5’ UTR of the human TAGAP gene has been identified as a genetic risk factor for a few diseases.

(a) In which transcripts is this SNP found?

(b) What is the least frequent genotype for this SNP in the Yoruba (YRI) population from the 1000 Genomes phase 3?

(c) What is the ancestral allele? Is it conserved in the 90 eutherian mammals?

(d) With which diseases is this SNP associated? Are there any known risk (or associated) alleles?

(a) Please note there is more than one way to get this answer. Either go to the Variation Table for the human TAGAP gene, and Filter variants to the 5’UTR, or search Ensembl for rs1738074 directly.

Once you’re in the Variation tab, click on the Genes and regulation link or icon.

This SNP is found in four transcripts of TAGAP. It is also intronic to five non-coding transcripts.

(b) Click on Population genetics at the left of the variation tab. (Or, click on Explore this variation at the left and click the Population genetics icon.)

In Yoruba (YRI), the least frequent genotype is CC at the frequency of 5.6%.

(c) Click on Phylogenetic context.

The ancestral allele is T and it’s inferred from the alignment in primates.

Select the 90 eutherian mammals EPO-Extended alignment and click on Apply.

A region containing the SNP (highlighted in red and placed in the centre) and its flanking sequence are displayed. The T allele is conserved in all but nine of the eutherian mammals displayed.

(d) Click Phenotype Data at the left of the Variation page.

This variation is associated with multiple sclerosis, celiac and white blood cell count. There are known risk alleles for both multiple sclerosis and celiac and the corresponding P values are provided. The allele A is associated with celiac disease. Note that the alleles reported by Ensembl are T/C. Ensembl reports alleles on the forward strand. This suggests that A was reported on the reverse strand in the original paper. Similarly, one of the alleles reported for Multiple sclerosis is G.

Exploring a SNP in human

The missense variation rs1801133 in the human MTHFR gene has been linked to elevated levels of homocysteine, an amino acid whose plasma concentration seems to be associated with the risk of cardiovascular diseases, neural tube defects, and loss of cognitive function. This SNP is also referred to as ‘A222V’, ‘Ala222Val’ as well as other HGVS names.

(a) Find the page with information for rs1801133.

(b) Is rs1801133 a Missense variation in all transcripts of the MTHFR gene? What is the amino acid change?

(c) Why are the alleles for this variation in Ensembl given as G/A and not as C/T, as in the literature?

(d) What is the major allele of rs1801133 in different populations?

(e) In which paper(s) is the association between rs1801133 and homocysteine levels described?

(f) According to the data imported from dbSNP, the ancestral allele for rs1801133 is G. Ancestral alleles in dbSNP are based on a comparison between human and chimp. Does the sequence at this same position in other primates confirm that the ancestral allele is G?

(a) Go to the Ensembl homepage (http://www.ensembl.org/).

Type rs1801133 in the Search box, then click Go. Click on rs1801133.

(b) Click on Genes and Regulation in the side menu (or the Genes and Regulation icon).

No, rs1801133 is Missense variant in nine MTHFR transcripts. Please note that this variant is multialleleic with two alternative alleles - as this table displays one consequence per row, each transcript is listed twice.

The amino acid change is A/V for allele A, and A/G for allele C.

(c) In Ensembl, the alleles of rs1801133 are given as G/A/C because these are the alleles in the forward strand of the genome. In the literature, the alleles are given as C/T/G because the MTHFR gene is located on the reverse strand. The alleles in the actual gene and transcript sequences are C/T/G. In Ensembl, the allele that is present in the reference genome assembly is always put first.

(d) Click on Population genetics in the side menu.

In all populations but one, the allele G is the major one. The exception is CLM (Colombian in Medellin; 1000 Genomes).

(e) Click on Phenotype Data in the left hand side menu.

The specific studies where the association was originally described is given in the Phenotype Data table. Links between rs1801133 and homocysteine levels were described in four papers. Click on the pubmed IDs pubmed:20031578, PMID:23696881, PMID:30339177 and pubmed:23824729 for more details.

(f) Click on Phylogenetic Context in the side menu.

Select Alignment: 12 primates EPO and click Apply.

Gorilla, bonobo, orangutan, chimp, macaque, gibbon, vervet, crab-eating macaque, mouse lemur, olive baboon and marmoset all have a G in this position.

Exploring a SNP in mouse

Madsen et al in the paper ‘Altered metabolic signature in pre-diabetic NOD mice’ (PloS One. 2012; 7(4): e35445) have described several regulatory and coding SNPs, some of them in genes residing within the previously defined insulin dependent diabetes (IDD) regions. The authors describe that one of the identified SNPs in the murine Xdh gene (rs29522348) would lead to an amino acid substitution and could be damaging as predicted as by SIFT (http://sift.jcvi.org/).

(a) Where is the SNP located (chromosome and coordinates)?

(b) What is the HGVS recommendation nomenclature for this SNP?

(c) Why does Ensembl put the C allele first (C/T)?

(d) Are there differences between the genotypes reported in NOD/LTJ and BALB/cByJ, according to the PERLGEN panel?

(a) Go to www.ensembl.org, type rs29522348 in the search box. Click on rs29522348 (Mouse Variation).

SNP rs29522348 is located on 17:74231988. In Ensembl, its alleles are provided as in the forward strand.

(b) Click on HGVS names to reveal information about HGVS nomenclature.

This SNP has got five HGVS names, one at the genomic DNA level (17:g.74231988C>T), three at the transcript level (ENSMUST00000024866.4:c.721G>A, ENSMUST00000233162.1:n.738G>A and ENSMUST00000233621.1:c.*284G>A) and one at the protein level (ENSMUSP00000024866.4:p.Val241Ile).

(c) In Ensembl, the allele that is present in the reference genome assembly is always put first (C is the allele for the reference mouse genome, strain C57BL/6J).

(d) Click on Sample genotypes is the left hand side menu. In the summary of genotypes by population, click on Show for PERLEGEN:MM_PANEL2, or search for the two strain names. There are indeed differences between the genotypes reported in those two different strains. The genotype reported in NOD/LTJ is T|T whereas in BALB/cByJ the genotype is C|C.

Exploring VNTR in human

Variable number tandem repeats (VNTRs) show high variation in the number of repeats in the population and are commonly used in forensics (DNA fingerprinting) and to study genetic diversity. (a) Go to the region from 3074666 to 3075100 bp on human chromosome 4. Which gene does it overlap? Which exon of this gene falls in this region?

(b) Configure this page to turn on Repeats (low), Simple repeats (Repeats (low)) and Tandem repeats (TRF) tracks in this view. Can you see any repeats in this exon? What tools were used to annotate the repeats according to the track information?

(c) Zoom in on the polyglutamine (PolyQ) tract or (CAG)n to see its sequence. How many CAG repeats can you see in the human reference assembly? Does this tract overlap any phenotype-associated variants? What is the identifier of this variant?

(d) Go to the variant tab of the phenotype-associated variant. What is the consequence ontology of this variant? Does the reference allele match the number of repeats you have just counted? What is the shortest and longest allele?

(e) Are there any phenotypes associated with this variant?

(a) Select Search: Human and type 4:3074666-3075100 in the text box (or alternatively type human 4:3074666-3075100 in the text box). Click Go.

Click on the golden transcript falling in this region. You can see its exon 1 of 67 of the huntingtin gene (HTT).

(b) Click Configure this page in the side menu then select: Repeats (low), Simple repeats (Repeats (low)) and Tandem repeats (TRF).

There are two types of tandem repeats in this exon: polyglutamine (PolyQ) tract or (CAG)n and polyproline (PolyP) tract or (CCG)n; annotated by two different methods. Click on the track names to find more about the tools used for annotation: RepeatMasker and Tandem Repeats Finder.

(c) Draw with your mouse a box around the polyglutamine (PolyQ) tract or (CAG)n. Click on Jump to region in the pop-up menu.

There are 19 CAG repeats in the human reference sequence overlapping rs71180116 indicated by a pink bar in the All phenotype-associated - short variants (SNPs and indels) track.

(d) Click on the rs71180116 ID to go to the variant tab. You can see in the summary page that this variant is classified as an inframe insertion. Either click + to show all of the alleles in the summary page or go to the Genes and regulation table. This variant has many alternative alleles which differ in the number of repeats. The first allele in the expanded Alleles section of the summary page or the first allele in the Codons column in the Genes and regulation table is the reference allele. It is composed of 19 CAG repeats just as in the Region in detail view. The shortest allele has 7 repeats, the longest has 55 repeats.

(e) Click on Phenotype data in the side menu. This variant is associated with Huntington disease, a trinucleotide repeat disorder (polyQ disease) caused by a pathogenic number of CAG repeats (above 36 copies) in a coding region of HTT.

VEP

We have identified five variants on human chromosome nine, C-> A at 128203516, an A deletion at 128328461, C->A at 128322349, C->G at 128323079 and G->A at 128322917.

We will use the Ensembl VEP to determine:

  • Have my variants already been annotated in Ensembl?
  • What genes are affected by my variants?
  • Do any of my variants affect gene regulation?

Go to the front page of Ensembl and click on the Variant Effect Predictor.

This page contains information about the VEP, including links to download the script version of the tool. Click on Launch VEP to open the input form:

The data is in VCF format:
chromosome coordinate id reference alternative

Put the following into the Paste data box:
9 128328460 var1 TA T
9 128322349 var2 C A
9 128323079 var3 C G
9 128322917 var4 G A
9 128203516 var5 C A

The VEP will automatically detect that the data is in VCF.

There are further options that you can choose for your output. These are categorised as Identifiers, Variants and frequency data, Additional annotations, Predictions, Filtering options and Advanced options. Let’s open all the menus and take a look.

Hover over the options to see definitions.

We’re going to select some options:

  • HGVS, annotation of variants in terms of the transcripts and proteins they affect, commonly-used by the clinical community
  • Phenotypes
  • Protein domains

When you’ve selected everything you need, scroll right to the bottom and click Run.

The display will show you the status of your job. It will say Queued, then automatically switch to Done when the job is done, you do not need to refresh the page. You can edit or discard your job at this time. If you have submitted multiple jobs, they will all appear here.

Click View results once your job is done.

In your results you will see a graphical summary of your data, as well as a table of your results.

The results table is enormous and detailed, so we’re going to go through the it by section. The first column is Uploaded variant. If your input data contains IDs, like ours does, the ID is listed here. If your input data is only loci, this column will contain the locus and alleles of the variant. You’ll notice that the variants are not neccessarily in the order they were in in your input. You’ll also see that there are multiple lines in the table for each variant, with each line representing one transcript or other feature the variant affects.

You can mouse over any column name to get a definition of what is shown.

The next few columns give the information about the feature the variant affects, including the consequence. Where the feature is a transcript, you will see the gene symbol and stable ID and the transcript stable ID and biotype. Where the feature is a regulatory feature, you will get the stable ID and type. For a transcription factor binding motif (labelled as a MotifFeature) you will see just the ID. Most of the IDs are links to take you to the gene, transcript or regulatory feature homepage.

This is followed by details on the effects on transcripts, including the position of the variant in terms of the exon number, cDNA, CDS and protein, the amino acid and codon change, transcript flags, such as MANE, on the transcript, which can be used to choose a single transcript for variant reporting, and pathogenicity scores. The pathogenicity scores are shown as numbers with coloured highlights to indicate the prediction, and you can mouse-over the scores to get the prediction in words. Two options that we selected in the input form are the HGVS notation, which is shown to the left of the image below and can be used for reporting, and the Domains to the right. The Domains list the proteins domains found, and where there is available, provide a link to the 3D protein model which will launch a LiteMol viewer, highlighting the variant position.

Where the variant is known, the ID of the existing variant is listed, with a link out to the variant homepage. In this example, only rsIDs from dbSNP are shown, but sometimes you will see IDs from other sources such as COSMIC. The VEP also looks up the variant in the Ensembl database and pulls back the allele frequency (AF in the table), which will give you the 1000 Genomes Global Allele Frequency. In our query, we have not selected allele frequencies from the continental 1000 Genomes populations or from gnomAD, but these could also be shown here. We can also see ClinVar clinical significance and the phenotypes associated with known variants or with the genes affected by the variants, with the variant ID listed for variant associations and the gene ID listed for gene associations, along with the source of the association.

For variants that affect transcription factor binding motifs, there are columns that show the effect on motifs (you may need to click on Show/hide columns at the top left of the table to display these). Here you can see the position of the variant in the motif, if the change increases or decreases the binding affinity of the motif and the transcription factors that bind the motif.

Above the table is the Filter option, which allows you to filter by any column in the table. You can select a column from the drop-down, then a logic option from the next drop-down, then type in your filter to the following box. We’ll try a filter of Consequence, followed by is then missense_variant, which will give us only variants that change the amino acid sequence of the protein. You’ll notice that as you type missense_variant, the VEP will make suggestions for an autocomplete.

You can export your VEP results in various formats, including VCF. When you export as VCF, you’ll get all the VEP annotation listed under CSQ in the INFO column. After filtering your data, you’ll see that you have the option to export only the filtered data. You can also drop all the genes you’ve found into the Gene BioMart, or all the known variants into the Variation BioMart to export further information about them.

VEP CFTR

Resequencing of the genomic region of the human CFTR (cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7) gene (ENSG00000001626) has revealed the following variants (alleles defined in the forward strand):

  • G/A at 7: 117,530,985
  • T/C at 7: 117,531,038
  • T/C at 7: 117,531,068

Use the VEP tool in Ensembl and choose the options to see SIFT and PolyPhen predictions. Do these variants result in a change in the proteins encoded by any of the Ensembl genes? Which gene? Have the variants already been found?

Go to www.ensembl.org and click on the link Tools at the top of the page. Currently there are nine tools listed in that page. Click on Variant Effect Predictor and enter the three variants as below:

7 117530985 117530985 G/A
7 117531038 117531038 T/C
7 117531068 117531068 T/C

Note: Variation data input can be done in a variety of formats. See more details here http://www.ensembl.org/info/docs/variation/vep/vep_formats.html

Click Run.

When your job is listed as Done, click View Results.

You will get a table with the consequence terms from the Sequence Ontology project (http://www.sequenceontology.org/) (i.e. synonymous, missense, downstream, intronic, 5’ UTR, 3’ UTR, etc) provided by VEP for the listed SNPs. You can also upload the VEP results as a track and view them on Location pages in Ensembl. SIFT and PolyPhen are available for missense SNPs only. For two of the entered positions, the variations have been predicted to have missense consequences of various pathogenicity (coordinate 117531038 and 117531068), both affecting CFTR. All the three variants have been already described and are known as rs1800078 and rs35516286 in dbSNP other sources (databases, literature, etc).

Viewing structural variants with the VEP

We have details of a genomic deletion in a breast cancer sample in VCF format:

13 32307062 sv1 . <DEL> . . SVTYPE=DEL;END=32908738

(a)  How many genes have been affected?

(b)  Does the SV cause deletion of any complete transcripts?

(c)  Display your variant in the Ensembl browser.

(a) Give your data a name, such as Patient deletion.

Paste 13 32307062 sv1 . <DEL> . . SVTYPE=DEL;END=32908738 into the Paste data field then hit Run.

13 genes have been affected.

(b) Use the Filters, selecting Consequence is transcript_ablation, Add.

Yes, there is deletion of complete transcripts of PDS5B, N4BP2L1, BRCA2, RNY1P4, IFIT1P1, ATP8A2P2, N4BP2L2, N4BP2L2-IT2, AL137247.1, AL137247.2 and AL138820.1.

(c) To view your variant in the browser click on the location link in the results table 13: 32307062-32908738. The link will open the Region in detail view in a new tab. If you have given your data a name it will appear automatically in red. If not, you may need to Configure this page and add it under Personal Data.

Comparative genomics

Let’s look at the homologues of human BRCA2. Search for the gene and go to the Gene tab.

Click on Gene tree, which will display the current gene in the context of a phylogenetic tree used to determine orthologues and paralogues.

Funnels indicate collapsed nodes. We can expand them by clicking on the node and selecting Expand this sub-tree from the pop-up menu.

We can also see the alignment of the sub-tree by clicking on Wasabi viewer, which will open a pop-up:

You can download the tree in a variety of formats. Click on the download icon in the bar at the top of the image to get a pop-up where you can choose your format.

We can look at homologues in the Orthologues and Paralogues pages, which can be accessed from the left-hand menu. If there are no orthologues or paralogues, then the name will be greyed out. Paralogues is greyed out for BRCA2 indicating that there are no paralogues available. Click on Orthologues to see the 176 orthologues available.

Choose to see only Rodents and related species orthologues by selecting the box. The table below will now only show details of rodent orthologues. Let’s look at mouse.

Links from the orthologue allow you to go to alignments of the orthologous proteins and cDNAs. Click on View Sequence Alignments then View Protein Alignment for the mouse orthologue.

Let’s look at some of the comparative genomics views in the Location tab. Go to the region 2:176087000-176202000 in human, which contains the HoxD cluster which is involved in limb development and is highly conserved between species.

You can turn on conservation scores and constrained elements. Click on Configure this page, then Comparative genomics and turn on the tracks for Constrained elements for 90 eutherian mammals EPO-Extended and Conservation score for 90 eutherian mammals EPO-Extended. Save and close the menu.

You can now see the conservation scores in pale pink. These were used to determine the peaks indicated in the constrained elements track in dark pink. This track indicates regions of high conservation between species, considered to be “constrained” by evolution.

We can also look at individual species comparative genomics tracks in this view by clicking on Configure this page.

Select BLASTz/LASTz alignments from the left-hand menu to choose alignments between closely related species. Turn on the alignments for Mouse, Chicken and Chimpanzee in Normal. Save and close the menu.

The alignment is greatest between closely related species.

We can also look at the alignment between species or groups of species as text. Click on Alignments (text) in the left hand menu.

Select Select an alignment to open the alignment menu.

Click through the links, Pairwise, Rodents & Lagomorphs, Rats and Mice to select Mouse reference (CL57BL6).

In this case there are two blocks aligned, Block 1 a large (115001 bp) alignment against mouse chr2 and one smaller block against mouse chr7. Click on Block 1.

You will see a list of the regions aligned, followed by the sequence alignment. Click on Display full alignment. Exons are shown in red.

To compare with both contigs visually, go to Region comparison.

To add species to this view, click on the blue Select species or regions button. Choose Mouse Reference again then close the menu.

You can configure this view for both species. Click on Configure this page and look in the top left of the menu.

The drop down allows you to configure each species separately.

We can view large scale syntenic regions from our chromosome of interest. Click on Synteny in the left hand menu.

Orthologues and gene trees for the human BRAF gene

(a) How many orthologues are predicted for the human BRAF in primates? How much sequence identity does the tarsier (Carlito syrichta) protein have to the human one? Can you tell which end of the BRAF protein is more conserved between these two species by looking at the orthologue alignment?

(b) Go to the Gene tree for this gene. View the Wasabi alignment of all the proteins in primates. Can you see a large gap in the alignment around position 450? Which species match the human sequence?

(a) Go to Ensembl homepage, choose human from the drop-down list and search for BRAF. Click through to the Gene tab view. On the Gene tab, click on Orthologues at the left side of the page to see all the orthologous genes.

There are 1:1 orthologues in 21 primates reported in the summary table.

Search for tarsier in the table below.

The percentage of identical amino acids in the tarsier protein (the orthologue) compared with the gene of interest. i.e. human BRAF (the target species/gene) is 93.95%. This is known as the Target %id. The identity of the gene of interest (human BRAF) when compared with the orthologue (tarsier BRAF, the query species/gene) is 88.48% (the Query %id). Note the difference in the values of the Target and Query %id reflects the different protein lengths for the human and tarsier BRAF genes.

Click on the View Sequence Alignments link in the Orthologue column to View Protein Alignment in Clustal W format.

Conserved amino acids are indicated by asteriks. The alignment around the N-terminus looks poorer, when compared to the C-terminus end.

(b) Click on Gene tree in the left hand menu. All of the primates are enclosed in a lilac box. Click on the furthest left node in the box to get a pop-up labelled Primates. Alternatively, scroll to the bottom of the page, and select Order from Collapse all the nodes at the taxonomic rank. Primates will appear as a red triangle. Click on Wasabi viewer in the pop-up menu to see the alignment. Scroll to position 450.

Greater bamboo lemur, mouse lemur, crab-eating macaque, Bolivian squirrel monkey, marmoset and Ma’s night monkey all match the human sequence.

Cow orthologues

Find the ABCC11 gene on the cow genome. (a) Go to the Location tab for this gene. View the Alignments (image) for the 46 eutherian mammals EPO. Do all the mammals have an alignment in this region? Can you spot a difference in the alignment between Pecora (including cattle, goats, sheep and deers) and the remaining mammals?

(b) Let’s now see this alignment as text. Go to Alignments (text) for the 46 eutherian mammals EPO. Sort the aligned blocks by genomic coordinates and view the 3’ portion of the ABCC11 gene (smallest coordinates). Does it support your previous conclusions? Export the alignment without ancestral sequences as ClustalW.

(c) Click on the Region in detail link at the left and turn on the tracks for Multiple alignments, Constrained elements and Conservation score for the 90 eutherian mammals EPO-Extended by configuring the page. What is the difference between the Multiple alignment track and the Constrained elements track? Which regions of the gene do most of the constrained element blocks match up to? Can you find more information on how the Constrained elements track was generated?

(a) Search for cow ABCC11 from the home page. Click on ABCC11 genomic coordinates 16:48165773-48247568:-1 in the search results to open the Location tab. Click on Alignments (image) at the left, and select the 46 eutherian mammals EPO multiple alignment by clicking on Select an alignment blue button. Scroll down to see the hidden and missing species.

All but 13 of the 46 mammals have an alignment at this region. ABCC11 gene model for the closely related Pecora species (cows, yak, goat, sheep and Yarkand deer) is longer when compared to the other species, with many additional exons at its 3’ end (left side of the image), which are absent in other taxa.

(b) Click on Alignments (text) in the left hand menu. The 46 eutherian mammals EPO alignment should be pre-selected. Scroll down to the table of alignment blocks. Sort the table by clicking on small arrows in the Location on Cow column header. The alignment blocks are now sorted by the genomic coordinates, with smalles coordiantes corresponding to the 3’ most end of ABCC11 (located on the reverse strand). Click on Block 3 to view the alignment.

Only 5 species have an alignment in this region, including cows, yak, goat, sheep and Yarkand deer, which is in agreement with our previous observation. Scroll up and click on Select another alignment blue button. Deselect Ancestral sequences by clicking on the x in the panel on the right, then Apply. Click on the blue Download alignment button, change File format to CLUSTALW, then Download.

(c) Click on Region in detail in the left hand menu. Turn on the Multiple alignments, Constrained elements and Conservation score for 90 eutherian mammals EPO-Extended tracks, all under the Comparative genomics in the Configure this page menu.

The 90 eutherian mammals EPO-Extended multiple alignment track is shown as pink block indicating that the whole region can be aligned at this locus. The GERP elements and GERP scores tracks show where the conserved sequence is located in the alignment. Conserved elements shown as pink boxes match up with exonic regions of the 5’-half of this cow gene (right side of the image). In general, exons tend to be highly conserved across taxa. Click on the track name and the i icon (information button) to read more about constrained elements (or any other data track).

Synteny

Start at Ensembl homepage. (a) Find the rhodopsin (RHO) gene in human. Go to the Location tab and click Synteny at the left. Are there any syntenic regions in dog? If so, which chromosomes are shown in this view?

(b) Stay in the Synteny view. Is there a homologue in dog for human RHO? Are there more genes in this syntenic block with homologues? Which dog chromosome is this human genomic region syntenic to?

(a) Search for human RHO from the home page. Click on RHO genomic coordinates 3:129528639-129535344:1 in the search results to open the Location tab. Click Synteny at the left and change the species to Dog next to the image.

Yes, there are multiple syntenic regions in dog to human chromosome 3, which is in the centre of this view. Dog chromosomes 6, 20, 23, 31, 33, and 34 have syntenic regions to human chromosome 3.

(b) Scroll down to the bottom of the page to see a list of homologous genes on both genomes.

There is no homologue of human RHO in dog. Click 15 upstream genes or 15 downstream genes to view neighbouring genes in this syntenic block. There are many neighbouring genes with homologues in dog. Human genes in this region are homologous to dog genes on chromosome 20, which is also indicated by the red boxes in the image above as this genomic block on human chromosome 3 is syntenic to dog chromosome 20.

Whole genome alignments

(a) Find the human BRCA2 gene and go to the Region in detail page. Turn on the BLASTz/LASTz alignment tracks for chicken, chimp, mouse and platypus. Does the degree of conservation between human and the various other species reflect their evolutionary relationship? Which parts of the BRCA2 gene seem to be the most conserved? Did you expect this?

(b) Have a look at the Conservation score and Constrained elements tracks for the set of 90 eutherian mammals and 63 amniota vertebrates. Do these tracks confirm what you already saw in the pairwise alignment tracks?

(C) Retrieve the genomic alignment (text) across 63 amniotes for a constrained element matching up with exon 15 of the golden transcript. Highlight the bases that match in >50% of the species in the alignment. Is this sequence exonic in all species?

(a) Select Human from the species selector drop-down list and type brca2 in the search box. Click Go. Click on 13:32315086-32400266:1 below BRCA2 (Human Gene) to go to the Region in detail page. Click Configure this page in the side menu, then BLASTz/LASTz alignments under the Comparative genomics menu. Select Chicken, Chimpanzee, Mouse and Platypus in Normal style.

Yes, the degree of conservation does reflect the evolutionary relationship between human and the other species; the highest degree of conservation is found in chimp, followed by mouse, platypus and chicken, respectively. Especially the exonic sequences of BRCA2 seem to be highly conserved between the various species, which is what is to be expected because these are supposed to be under higher selection pressure than intronic and intergenic sequences.

(b) Click Configure this page in the side menu, then Conservation regions under the Comparative genomics menu. Select Conservation score and Constrained elements for 90 eutherian mammals EPO-Extended and 65 amniota vertebrates Mercator-Pecan.

Both the Conservation score and Constrained elements tracks largely correspond with the data seen in the pairwise alignment tracks; all exons of the BRCA2 gene show a high degree of conservation (note the UTRs which are not conserved).

(c) Click on exons of the golden transcript (ENST00000380152.8) to reveal their rank in transcript. Exon 15 can be found in the middle. Click on a constrained element in 63 way GERP elements track matching up with this exon. Click on View alignments (text) in the pop-up menu, then Configure this page in the side menu. Select Show conservation regions to highlight bases matching in majority of the species in this alignment.

Exons are indicated by red lettering. All but Indian cobra and eastern brown snake have exonic sequence in this region.

Regulation

We’re going to have a look for regulatory features in the region of a gene and investigate their activity in different cell types. We’ll start by searching for the gene KPNA2 and jumping to the location tab. Zoom out a little to see the gene plus some flanking regions.

The Regulatory Build is shown by default.

In this region we can see a number of regulatory features, including a red promoter with pink promoter flanks, cyan CTCF binding sites, yellow enhancers and lilac TF binding sites (don’t worry if you have zoomed out further or not as far and can see more/less). Refer to the legend at the bottom to see what the colours mean.

You can also click on the regulatory features to learn more. Click on the red promoter to get a pop-up.

Click on the stable ID, ENSR00000097453, to jump to the Regulation tab.

Black and grey lines indicate the positions of transcription factor binding motifs (TFBMs). Black lines are verified, which means there is evidence of the TF binding at this locus in at least one studied cell type, whereas grey ones have not been observed. Click on a TFBM then the matrix ID to see the matrix as a pop-up window.

Close the motif pop-up and scroll down the page. We can see that this promoter is active in one out of the 118 cell types currently in Ensembl.

We can explore more detailed data in Details by cell type – click on the button at the top.

At the moment the page is not displaying any data as we haven’t chosen any cell types. Click on Configure Cell/Tissue to add more to the view.

We can add cells by clicking on them. Find them using the search or the alphabet ribbon. Let’s add a cell type where the promoter is inactive, aorta, and one where it’s active astrocytes. Once you’ve selected the cells, they will appear in the menu on the right, where you can easily view the list by clicking on the + and deselect them.

To choose the experiments to see data on, click on the Experiments tab at the top of the menu. You can navigate this the same as the Cell/Tissue tab, except that you have to choose between Histone modifications, Open Chromatin and Transcription Factors. Let’s Select all in all categories.

When you’ve chosen your experiments and cells, you can click on the green Configure track display button.

Now we can see the active feature in astrocytes compared to the inactive feature in aorta.

Gene regulation: Human INSIG1 and BLACE

(a) Find the Location tab (Region in detail page) for the region between the genes INSIG1 and BLACE. Are there any predicted enhancers in this region?

(b) Go to the Regulation tab for the enhancer ENSR00001133586. How many cell types is this enhancer active in? Are there any cell types where its activity is repressed?

(c) Go to the Details by cell type page. Take a look at the histone modifications across this enhancer in neutro myelocyte cells, where this enhancer is active, compared to neutrophil (CB) cells, where it is poised. What differences can you observe?

(d) Go back to the Summary page. Are there any verified transcription factor binding motifs in this enhancer? In what cells?

(a) Search for human INSIG1 from the home page. Click on INSIG1 genomic coordinates 7:155297776-155310235:1 in the search results to open the Location tab.

In the region overview, drag out a box to encompass the neighbouring BLACE gene. Have a look at the Regulatory Build track.

There is one yellow enhancer in the region between these genes.

(b) Click on the enhancer to get a pop-up with its ID and other information. Click on the ID ENSR00001133586 to open the Regulation tab.

Scroll down to see the summary of regulatory activity across different cell types.

ENSR00001133586 is active in neutro myelocyte cells. It is repressed in 34 cell types.

(c) Click on Details by cell type at the top of the page or in the left-hand menu.

Choose cells by clicking on Configure Cell/Tissue blue button, then selecting neutro myelocyte in which this enhancer is active and neutrophil (CB) in which it is poised.

Add experiment tracks by clicking on Experiments tab and Select all under Histone. Click Configure track display, then View tracks to load the page.

Both cell types have H3K27me3, H3K4me1 and H3K9me3 modifications at this locus, while neutro myelocyte cells also have H3K27ac and H3K36me3 modifications. Different clusters of peaks indicate different epigenetic profiles, which might explain the difference in the enhancer activity between these two cell types.

(d) Go back to the Summary view. In the Motif features track there are two black markers indicating verified TF motifs.

Click on them to tell which motifs and which cells.

The two motifs are both verified in K562 cells and bind a number of different TFs. One binds ELF1, ELF2, ELK1, FLI1, ERG, ETS1, ETV6, FOXO1::ELK3, FOXO1::ETV1, ETV1, ETV2, ERF, ELK3, ETV3, GABPA, ETS2, ELK4, FEV, ETV5 and ETV4. The other binds ETV7, ETS1 and ELK1::SPDEF.

Regulatory features in human

(a) Search for the regulatory feature ENSR00000262400. What type of feature is this? What is its genomic location?

(b) Which cell types is this feature inactive or repressed in? Look at the Details by cell type, why do you think it has been called differently in these cell types when compared to all other cells?

(c) Why do so many cells have this feature listed as NA on the summary page?

(a) Search for ENSR00000262400 from the home page. Click on the search result to open the Regulation tab.

ENSR00000262400 is a CTCF binding site found at Chromosome 11: 1,998,201-2,003,400, which can be found at the top of the Summary page.

(b) Scroll down to see the summary of regulatory activity across different cell types.

The CTCF binding site is inactive in H1-hESC_3 and HepG2 cells. It is repressed in A673.

Click on Details by cell type at the top of the page or in the left-hand menu. Choose cells by clicking on Configure Cell/Tissue blue button, then Selecting all 148 cell types. Add the CTCF binding track by clicking on Experiments tab, Transcription factors and CTCF. Click Configure track display, then View tracks to load the page.

CTCF-binding has been observed in cells where it is active and in some cells where it is poised or inactive. It cannot be observed in cells where it is repressed.

(c) Note that many cell types have this feature represented as white block with no corresponding CTCF signal or peaks.

Cells which do not have CTCF ChIP-seq data cannot have an activity listed for this feature.

BioMart

Follow these instructions to guide you through BioMart to answer the following query:

You have three questions about a set of human genes:
ESPN, MYH9, USH1C, CISD2, THRB, WHRN
(these are HGNC gene symbols. More details on the HUGO Gene Nomenclature Committee can be found on http://www.genenames.org)

  1. What are the NCBI Gene IDs for these genes?
  2. Are there associated functions from the GO (gene ontology) project that might help describe their function?
  3. What are their cDNA sequences?

Click on BioMart in the top header of a www.ensembl.org page to go to: www.ensembl.org/biomart/martview

You cannot choose any filters or attributes until you’ve chosen your dataset. Your dataset is the data type you’re working with. In this case we’re going to choose human genes, so pick Ensembl Genes then Human genes from the drop-downs.

Now that you’ve chosen your dataset, the filters and attributes will appear in the column on the left. You can pick these in any order and the options you pick will appear.

Click on Filters on the left to see the available filters appear on the main page. You’ll see that there are loads of categories of Filters to choose from. You can expand these by clicking on them. For our query, we’re going to expand GENE.

Our input data is a list of identifiers, so we’re going to use the Input external references ID list filter. This allows us to input a list of identifiers from different databases. We need to choose what kind of identifier we’re using, so that BioMart can look up the right column in a data table. You can pick these from a drop-down list, which lists the type of identifier with an example of how it looks. For our query, we have a list of gene names, so we need to pick Gene Name(s).

To check if the filters have worked, you can use the Count button at the top left, which will show you how many genes have passed the filter. If you get 0 or another number you don’t expect, this can help you to see if your query was effective.

To choose the attributes, expand this in the menu. There are six categories for human gene attributes. These categories are mutually exclusive, you cannot pick attributes from multiple categories. This means that we need to do two separate queries to get our GO terms and NCBI IDs, and to get our cDNA sequences.

The Ensembl gene and transcript IDs, with and without version numbers are selected by default. The selected attributes are also listed on the left.

We can choose the attributes we want by clicking on them. For our query, we’re going to select:

  • GENE
    • Gene Name
  • EXTERNAL
    • NCBI gene ID
    • GO term accession
    • GO term name
    • GO term definition

We need to select the Gene Name in order to get back our original input, as this is not returned by default in BioMart. The order that you select the attributes in will define the order that the columns appear in in your output table.

You can get your results by clicking on Results at the top left.

The results table just gives you a preview of the first ten lines of your query. This allows the results to load quickly, so that if you need to make any changes to your query, you don’t waste any time. To see the full table you can click on View ## rows. You can also export the data to an xls, tsv, csv or html file. For large queries, it is recommended that you export your data as Compressed web file (notify by email), to ensure your download is not disrupted by connection issues.

You can see multiple rows per gene in your input list, because there are multiple transcripts per gene and multiple GO terms per transcript.

To get the cDNA sequences, go back to the Attributes then select the category Sequences and expand SEQUENCES.

When you select the sequence type, the part of the transcript model you’ve chosen will be highlighted in the grpahic.

Choose cDNA sequences, then expand HEADER INFORMATION to add Gene Name to the header. Then hit Results again.

For more details on BioMart, have a look at this publication:

Kinsella, R.J. et al
Ensembl BioMarts: a hub for data retrieval across taxonomic space.
http://europepmc.org/articles/PMC3170168

Finding genes by protein domain

Find mouse proteins with Signalp cleavage sites located on chromosome 9.

As with all BioMart queries you must select the dataset, set your filters (input) and define your attributes (desired output). For this exercise: Dataset: Ensembl genes in mouse Filters: Signalp cleavage sites on chromosome 9 Attributes: Ensembl gene and transcript IDs and gene names

Go to the Ensembl homepage (http://www.ensembl.org) and click on BioMart at the top of the page. Select Ensembl genes as your database and Mouse genes as the dataset. Click on Filters on the left of the screen and expand REGION. Change the chromosome to 9. Now expand PROTEIN DOMAINS, also under filters, and select Limit to genes, choosing with With Cleavage site (Signalp) from the drop-down and then Only. Clicking on Count should reveal that you have filtered the dataset down to 216 genes.

Click on Attributes and expand GENE. Select Gene name. Now click on Results. The first 10 results are displayed by default; Display all results by selecting ALL from the drop down menu.

The output will display the Ensembl gene ID, Ensembl Transcript ID and gene names of all proteins with a Signalp cleavage site on mouse chromosome 9. If you prefer, you can also export as an Excel sheet by using the Export all results to XLS option.

Exporting homologues with BioMart

For a list of Ciona savignyi Ensembl genes, export the human orthologues.

ENSCSAVG00000000002, ENSCSAVG00000000003, ENSCSAVG00000000006, ENSCSAVG00000000007, ENSCSAVG00000000009, ENSCSAVG00000000011

Do all of these genes have a homologue in human?

Go to BioMart and click New. Choose the Ensembl Genes database. Choose the C.savignyi genes (CSAV 2.0) dataset.

Click on Filters in the left panel. Expand the GENE section by clicking on the + box. Enter the gene list in the Input external references ID list box. Gene stable ID(s) should be preselected.

Click on Attributes in the left panel. Select the Homologues attributes at the top of the page. Expand the GENE section by clicking on the + box. Deselect Gene stable ID version, Transcript stable ID and Transcript stable ID version. Expand the ORTHOLOGUES [F-J] section by clicking on the + box. Select Human gene stable ID.

Click Results. Select View: All rows as HTML.

All but ENSCSAVG00000000006 have a homologue in human.

BioMart Convert IDs

BioMart is a very handy tool when you want to convert IDs from different databases. The following is a list of 29 IDs of human proteins from the NCBI RefSeq database:

NP_001218 NP_203125 NP_203124 NP_203126 NP_001007233 NP_150636 NP_150635 NP_001214 NP_150637 NP_150634 NP_150649 NP_001216 NP_116787 NP_001217 NP_127463 NP_001220 NP_004338 NP_004337 NP_116786 NP_036246 NP_116756 NP_116759 NP_001221 NP_203519 NP_001073594 NP_001219 NP_001073593 NP_203520 NP_203522

Generate a list that shows to which Ensembl Gene IDs and to which gene names these RefSeq IDs correspond. Do these 29 transcripts correspond to 29 genes?

Click New. Choose the ENSEMBL Genes database. Choose the Human genes (GRCh38) dataset.

Click on Filters in the left panel. Expand the GENE section by clicking on the + box. Select Input external references ID list - RefSeq peptide ID(s) and enter the list of IDs in the text box (either comma separated or as a list). HINT: You may have to scroll down the menu to see these. Count shows 11 genes (remember one gene may have multiple splice variants coding for different proteins, that is the reason why these 29 proteins do not correspond to 29 genes).

Click on Attributes in the left panel. Select the Features attributes page. Expand the External section by clicking on the + box. Select HGNC symbol and RefSeq Peptide ID from the External References section.

Click the Results button on the toolbar. Select View All rows as HTML or export all results to a file.

Export structural variants

You can use BioMart to query variants, not just genes. (Make sure you use the right Datasets.)

(a) Export the study accession, source name, chromosome, sequence region start and end (in bp) of human structural variations (SV) on chromosome 1, starting at 130,408 and ending at 210,597.

(b) In a new BioMart query, find the alleles, phenotype descriptions, and associated genes for the human SNPs rs566014072 and rs754099015. Can you view this same information in the Ensembl browser?

(a) Choose Ensembl Variation and Human Structural Variants (GRCh38).

Filters: Region: Chromosome 1, Base pair start: 130408, Base pair end: 210597

Count shows 87 structural variants.

Attributes: Structural Variation (SV) Information: DGVa Study Accession and Source Name, Structural Variation (SV) Location: Chromosome/scaffold name, Chromosome/scaffold position start (bp) and Chromosome/scaffold position start (bp) end (bp).

(b) Choose Ensembl Variation and Human Short Variation (SNPs and indels) (GRCh38).

Filters: Filter by Variation name enter: rs566014072, rs754099015

Attributes: Variant Name, Variant Alleles, Phenotype description and Associated gene.

You can view this same information in the Ensembl browser. Click on one of the variation IDs (names) in the result table. The variation tab should open in the Ensembl browser. Click Phenotype Data.

Find genes associated with array probes

Forrest et al performed a microarray analysis of peripheral blood mononuclear cell gene expression in benzene-exposed workers (Environ Health Perspect. 2005 June; 113(6): 801–807). The microarray used was the human Affymetrix U133A/B (also called U133 plus 2) GeneChip. The top 25 up-regulated probe-sets were:

207630_s_at 221840_at 219228_at 204924_at 227613_at 223454_at 228962_at 214696_at 210732_s_at 212370_at 225390_s_at 227645_at 226652_at 221641_s_at 202055_at 226743_at 228393_s_at 225120_at 218515_at 202224_at 200614_at 212014_x_at 223461_at 209835_x_at 213315_x_at

(a) Retrieve for the genes corresponding to these probe-sets the Ensembl Gene and Transcript IDs as well as their HGNC symbols and descriptions.

(b) In order to analyse these genes for possible promoter/enhancer elements, retrieve the 2000 bp upstream of the transcripts of these genes.

(c) In order to be able to study these human genes in mouse, identify their mouse orthologues. Also retrieve the genomic coordinates of these orthologues.

(a) Click New. Choose the ENSEMBL Genes database. Choose the Human genes (GRCh38) dataset.

Click on Filters in the left panel. Expand the GENE section by clicking on the + box. Select Input microarray probes/probesets ID list - Affy hg u133 plus 2 probeset ID(s) and enter the list of probeset IDs in the text box (either comma separated or as a list).

Count shows 26 genes match this list of probesets.

Click on Attributes in the left panel. Select the Features attributes page. Expand the GENE section by clicking on the + box. In addition to the default selected attributes, select Description. Expand the External section by clicking on the + box. Select HGNC symbol from the External References section and AFFY HG U133-PLUS-2 from the Microarray Attributes section.

Click the Results button on the toolbar. Select View All rows as HTML or export all results to a file. Tick the box Unique results only.

Your results should show that the 25 probes map to 27 Ensembl genes.

(b) Don’t change Dataset and Filters – simply click on Attributes.

Select the Sequences attributes page. Expand the SEQUENCES section by clicking on the + box. Select Flank (Transcript) and enter 2000 in the Upstream flank text box. Expand the Header information section by clicking on the + box. Select, in addition to the default selected attributes, Description and gene name.

Note: Flank (Transcript) will give the flanks for all transcripts of a gene with multiple transcripts. Flank (Gene) will give the flanks for one possible transcript in a gene (the most 5’ coordinates for upstream flanking).

Click the Results button on the toolbar.

(c) You can leave the Dataset and Filters the same, and go directly to the Attributes section:

Click on Attributes in the left panel. Select the Homologues attributes page. Expand the GENE section by clicking on the + box. Select Gene name. Deselect Ensembl Transcript ID. Expand the ORTHOLOGUES [K-O] section by clicking on the + box. Select Mouse Ensembl Gene ID, Mouse Chromosome Name, Mouse Chr Start (bp) and Mouse Chr End (bp).

Click the Results button on the toolbar. Select View All rows as HTML or export all results to a file.

Your results should show that for most of the human genes at least one mouse orthologue has been identified.

Exporting paralogues with BioMart

Export a list of all human genes on chromosome 14 which have a paralogue, including the gene names, the last common ancestor and the identity between the genes. How many genes on chromosome 14 have a paralogue?

Go to BioMart and click New. Choose the Ensembl Genes database. Choose the Human genes dataset.

Click on Filters in the left panel. Expand the REGION section by clicking on the + box and select Chromosome/scaffold14. Under MULTI SPECIES COMPARISONS select Homologue filtersParalogous Human Genes: Only. Click the Count button in the side menu.

There are 805 genes on chromosome 14 which have a paralogue.

Click on Attributes in the left panel. Select Homologues from the six options at the top. Expand the GENE section by clicking on the + box. Deselect Transcript stable ID and Transcript stable ID version and select Gene name. Under PARALOGUES select Human paralogue gene stable ID, Human paralogue associated gene name, Paralogue last common ancestor with Human, Paralogue %id. target Human gene identical to query gene and Paralogue %id. query gene identical to target Human gene. Click the Results button on the toolbar. Select View: All rows as HTML or Export all results to a File.

Exporting regulatory features with BioMart

Using the Human Regulatory Features dataset, export a list of all enhancers falling in cytogenetic band q13.2 on chromosome 22 and their activity in Aorta. How many of them are active?

Go to BioMart and click New. Choose the Ensembl Regulation database. Choose the Human Regulatory Features dataset.

Click on Filters in the left panel. Expand the REGULATORY FEATURES section by clicking on the + box and select the following:

  • Chromosome - 22
  • Karyotype band: Band start – q13.2, Band end - q13.2
  • Feature TypeEnhancer
  • Epigenome nameaorta

Click on Attributes in the left panel. Select Chromosome/scaffold name, Start (bp), End (bp), Feature type, Regulatory stable ID, Activity and Epigenome name. Click the Results button to see the results table. Select View: All and choose to see Unique results only.

There is only one enhancer active in aorta in this cytogenetic band: ENSR00001239875.

Exporting histone modification sites with BioMart

Using the Human Regulatory Evidence dataset, export a list of all H3K9me3 modified loci on chromosome Y in Aorta. What is the source of this evidence?

Go to BioMart and click New. Choose the Ensembl Regulation database. Choose the Human Regulatory Evidence dataset.

Click on Filters in the left panel. Expand the REGULATORY EVIDENCE section by clicking on the + box and select Chromosome - Y, Feature Type – H3K9me3, and Epigenome – aorta.

Click on Attributes in the left panel. Select Chromosome/scaffold name, Start (bp), End (bp), Feature type, Epigenome name and Project name. Click the Results button to see the results table. Select View: All rows as HTML or Export all results to a File.

This data comes from the Roadmap Epigenomics.