To annotate using Ensembl Gene ID, you have to access to Ensembl Biomart through this link. Then, follow these steps:
Choose Ensembl Genes database.
Choose the dataset corresponding to the species which you are working with.
On the right menu, select Filters > Gene > Input external references. Copy your Ensembl Gene IDs in the white dialog or upload a text file containing your Ensembl Gene IDs.
Then, select, for example, Attributes > Gene > Gene name on Ensembl options. If you want to annotate, for instance, GO terms, you have to click on External and select the options you find useful such as GO domain, GO term accession and GO term name. There are a lot of options that you can select.
Once you have selected all attributes you need, click on Count and then on Results. On "Export all results to", click on "Unique results only" and the CSV option. Click on "Go" to download the results.
Before using the Worksheet tool, replace the colon by semicolon using a text editor.
Open the Worksheet tool of GPRO suite and open the CSV file that contains your differential expressed genes.
Click on File > Import > Combine worksheet. Select the key column of your CSV file (in this case is the column that contains the Ensembl Gene ID), select "Single file" option, the input file (this is the file you have downloaded from Biomart) and the output folder. Finally, select the key column of the downloaded file (in this case the column name is "Gene stable ID"), select the columns you want to export to your output file and click on the "OK" button.
