Finding genes by protein domain
Find chicken proteins with transmembrane domains 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 chicken
Filters: Transmembrane proteins on chromosome 9
Attributes: Ensembl gene and transcript IDs and Associated 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 Chicken 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 Transmembrane domains from the drop-down and then Only. Clicking on Count should reveal that you have filtered the dataset down to 139 genes.
Click on Attributes and expand GENE. Select Associated 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 Associated gene names of all proteins with a transmembrane domain on chicken chromosome 9. If you prefer, you can also export as an Excel sheet by using the Export all results to XLS option.