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/scaffold – 14. Under MULTI SPECIES COMPARISONS select Homologue filters – Paralogous Human Genes: Only. Click the Count button in the side menu.
There are 806 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.
