Introduction to Ensembl Genome Browser/Biomart

1. Click on « configure this page » (left-bottom menu)
2. Select Yes for « Show variations: »

1. Click on Filters (left panel),
2. Expand the “GENE” section
3. Select “Input external references ID list”, select “Gene Name(s)“ in the drop down list and enter IDH1.
4. Click on Count in the top left panel . You should get 1/67130 Genes.
5. Click on Attributes (left menu)
6. Select “Features” (selected by default)
7. Select Gene stable ID, Transcript stable ID, Gene Name
8. Click on Results (top left menu)

9 transcripts are found

You can leave the Dataset and Filters the same, and go directly to the Attributes section

1. Click on Attributes (left panel)
2. Select “Sequences”
3. Expand the SEQUENCES section
4. Select Exon sequences
5. Expand “Header Information”
6. Unselect “Gene stable ID” (Gene Information)
7. Select Gene name (Gene Information), Transcript stable ID (Transcript Information) and Exon stable ID (Exon Information).
8. Click on Results

You can leave the Dataset and Filters the same, and go directly to the Attributes section

1. Click on Attributes (left panel)
2. In the SEQUENCES section: select Coding sequence
3. In the “Header Information”: unselect Gene name (Gene Information) and keep Transcript stable ID (Transcript Information) and Exon stable IDs (Exon Information) selected.
4. Click on Results

You can leave the Dataset and Filters the same, and go directly to the Attributes section

1. Click on Attributes (left panel)
2. Select “Features” (selected by default)
3. In the GENE section: Gene stable ID, Transcript stable ID and Gene Name should be selected
4. Expand the EXTERNAL section
5. Select GO Term Name, GO domain and GO Term Accession
6. Click on Results

You can leave the Dataset and Filters the same, and go directly to the Attributes section

1. Click on Attributes (left panel)
2. Select “Variant (Germline)”
3. In the GENE section: Gene stable ID, Transcript stable ID and Gene Name should be selected
4. Expand the GERMLINE VARIANT INFORMATION section
5. Select Variant Name, Variant Alleles, Minor allele frequency, Chromosome/scaffold name, Chromosome /scaffold position start (bp), Chromosome/scaffold position end (bp), Variant Consequence
6. Click on Results

In Ensembl/BioMart, create a new request using an archive of Ensembl v84.

1. Click on Filters (left panel)
2. Expand the GENE section
3. Select “Input external references ID list” and select “Ensembl Gene ID(s)” in the drop down list
4. Click on “Browse” and select the file siMitfvssiLuc.up.txt
5. Click on “Count” (top left button). You should have: 3792/66232 Genes
6. Click on Attributes (left panel)
7. Select “Features” (selected by default), select Ensembl Gene ID, Chromosome Name, Gene Start (bp), Gene End (bp), Strand, Associated Gene Name and Gene type.
8. Click on Results
9. Select Compressed file (.gz) in the drop down menu. Click on Go to download the resulting file.

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

1. Click on Attributes (left panel)
2. Select “Sequences”
3. Expand the SEQUENCES section
4. Select Flank (Transcript) and enter 200 in the Upstream flank text box
5. Expand the Header information section
6. Select, in addition to the default selected attributes, Description and Associated Gene Name

<WRAP tip> 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) <WRAP>

In Ensembl/BioMart, create a new request

1. Click on Filters (left panel)
2. Expand the REGION section
3. Select “Multiple Chromosomal Regions” and enter 2:208226227:208276270 in the text box
4. Click on Count

4 genes are found

In Ensembl/BioMart, create a new request (see slide 2.)

1. Click on Filters (left panel)
2. Expand the REGION section
3. Select “Chromosome” and multiple select 1 → MT (click and drag). This corresponds to 57992 / 63967 Genes
4. Click on Attributes (left panel)
5. Select “Features” (selected by default)
6. In GENE, select Gene stable ID, Chromosome/scaffold name, Gene Start (bp), Gene End (bp), strand and Gene Name
7. Click on Results

1. Click New.
2. Choose the ENSEMBL Genes 91 database.
3. Choose the Homo sapiens genes (GRCh38.p10) dataset.

1. Click on Filters in the left panel.
2. Expand the GENE section by clicking on the + box.
3. Select ID list limit - RefSeq protein ID(s) and enter the list of IDs in the text box (either comma separated or as a list).
4. HINT: You may have to scroll down the menu to see these.

1. Count shows 4 genes (remember one gene may have multiple splice variants coding for different proteins, that is the reason why these 11 do not correspond to 11 genes).

1. Click on Attributes in the left panel.
2. Select the Features attributes page.
3. Expand the External section by clicking on the + box.
4. Select Gene name and RefSeq Protein ID from the External References section.

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

• Click New.
• Choose the ENSEMBL Genes 91 database.
• Choose the Homo sapiens genes (GRCh38.p10) dataset.

• Click on Filters in the left panel.
• Expand the GENE section by clicking on the + box.
• Select ID list limit - 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 10 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 Gene name 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 11 probes map to 8 Ensembl genes.

• 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 Homologs attributes page.
• Expand the GENE section by clicking on the + box.
• Select Associated Gene Name.
• Deselect Ensembl Transcript ID.
• Expand the ORTHOLOGS section by clicking on the + box.
• Select Mouse Ensembl Gene stable ID, Mouse chromosome/scaffold name, Mouse chromosome/scaffold Start (bp) and Mouse chromosome/scaffold End (bp).

• Click the Results button on the toolbar.
• Check the box Unique results only. 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.