Retreiving Annotation via biomart

Annotation from BioMart with Ensembl names is most flexible way to retrieve tabular annotation for an organism.

1. The Biomart start page should look like …

   

2. First select the dataset, for gene expression experiment select Ensembl Genes 114 (version 114). The current version as of this workshop.

   

3. Then the Organism, Here Mouse genes which is based on the GRCm39 genome.

   

4. You can choose to filter to only a subset of genes. Or a chromosome, or regions. We won’t filter here. BY default, all genes in the genome are selected.

   

   

5. Next select the attributes you want in the table.

   

6. Expand the ‘GENE’ tab, and select the attributes you want to retrieve. HERE recreate the list you see on the left side.

   

7. Click “Results” (Top left -ish).

   

8. Select “GO”, to download a tab-separated value (tsv) file.

   

9. The file will save as “mart_export.txt”, put the file into our working directory, rename to “ensembl_mm_114.txt” and open the file in Excel to view the annotation.