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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 217 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.