BioMart FAQs

Q: I have two Ensembl gene IDs, ENSG00000162367 and ENSG00000187048. How do I get their gene names from HGNC, IDs from EntrezGene, and any probes that contain these gene sequences from the Affymetrix microarray platform HC G110?

A:

• Database: Ensembl
• Dataset: Homo sapiens genes
• Filters:GENE: ID List limit box

  Header: Ensembl Gene IDs, Enter the gene names into the box.

• Attributes: EXTERNAL: External References

  Select 'HGNC Symbol' and 'EntrezGene ID'

• Attributes: EXTERNAL: Microarray Attributes

Select 'Affy HC G110'

Click Results

Q: How do I export protein sequence on human chromosome 1?

A:

• Database: Ensembl
• Dataset: Homo sapiens genes
• Filters:Filters:REGION

  Select Chromosome 1

• Attributes: Sequences page:SEQUENCES panel

  Select 'Protein'

  Click Results

Q: How can I find all Ensembl genes and transcript IDs between the markers MCW0423 and MCW0431 on chicken chromosome 1? Could I see IDs from the Gene Ontology Consortium, as well?

A:

• Database: Ensembl
• Dataset: Gallus gallus genes
• Filters:REGION:

  Chromosome 1

  Marker Start MCW0423

  Marker End MCW0431

• Attributes: EXTERNAL

  Select 'GO ID' in each catagory

Click Results

Q: Can I export all variations associated with the human CFTR gene, along with SNP, or Single Nucleotide Polymorphism, alleles?

A:

• Database: Ensembl because you filter on a gene, not a SNP!
• Dataset: Homo sapiens genes
• Filters:GENE: ID List limit box

  Header: HGNC symbol, Enter 'CFTR' into the box.

• Attributes: Variations page

  GENE: Deselect Ensembl Transcript ID

  GENE ASSOCIATED SNPs: Select Reference ID and Allele

Click Results

Q: For all SNPs on mouse chromosome 1, I would like the SNP name, allele and base pair position.

A:

• Database: Variation
• Dataset: Mus musculus SNPs
• Filters:REGION

  Chromosome 1

• Attributes: SNPs page

  SNP:Allele

Click Results

Q:Advanced Mart I would like mouse SNPs on an alternate strain. The reference strain Ensembl uses is C57BL/6J. How do I export SNPs between two other strains A/J and BalbC?

A:

• Database: Variation
• Dataset: Mus musculus SNPs
• Filters:none
• Attributes: Strain polymorphisms page

  Reference strain:A/J

  Strains to compare: Balb/c

Click Results

Q:Advanced Mart How do I export all mouse homologues for human genes, starting with HGNC symbols Calm1, Calm2 and Calm3? Could I see MGI symbols for the mouse homologues?

A:

• Database: Ensembl
• Dataset: Homo sapiens genes
• Filters:GENE: ID List Limit box

  Header: HGNC Symbol, enter in calm1, calm2, calm3... or Browse to upload a file.

• Attributes: Homologs page

  MOUSE ORTHOLOGS

  Orthologue Attributes: Mouse Ensembl Gene ID

ADVANCED MART:

Select the secondary, linked Dataset.

• Additional Dataset: Mus musculus genes
• Additional Filters:None
• Additional Attributes: EXTERNAL:External References

  MGI symbol

  Click Results