Gene Ontology Data

How do I find the GO annotations for my set of genes?

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This assumes that you have successfully uploaded or created your list of genes. If you require help with this, please see Lists - Upload a list section for more details.

To find the GO term annotations for your genes, it's easier to start by finding a template search specifically for this purpose.

1. From the HumanMine homepage, select the ‘Templates’ tab from the top navigation bar.
2. From the list of templates, we are looking for the Gene → GO terms template. If you cannot see it immediately, enter the term ‘GO’ into the search box to filter the results.
3. Click on the template name or ‘View >>’ at the bottom left corner to expand the template details, including the fillable form.
4. Select a list that you wish to run the search with, then press ‘View Rows’.

Modifying and filtering your search results

This template search returns GO term annotations for all three GO ontologies and other GO attributes, such as evidence code and qualifier. You may wish to further filter your results on some of these attributes or add additional attributes to the search, such as annotation extension or the GO ‘with’ attribute. The following examples illustrate how to do this.

How do I filter my results to show only GO annotations from the ‘biological process’ ontology?

The easiest way to filter your results is by using the filter functions in the results table.

1. You can accomplish this by clicking on the graph iconin the Ontology Term Namespace column header.
2. Then select ‘biological_process’ using the checkbox to the left, and click the ‘Filter’ button.
3. To return to your original results, either remove the filter by clicking on the blue filter iconin the column header or use the UNDO button above the results table.

How do I filter my results to remove those with the IEA - Inferred from Electronic Annotation - evidence code?

You can accomplish this in three ways:

• Using the column summary

1. Click on the column summary/graph iconin the Code column header.
2. Select all evidence codes except the IEA code.
3. Click Filter.

• Using the Code column filter icon

1. Click on the filter iconin the Code column header.
2. Use the left drop-down menu to choose the != option.
3. Use the right drop-down list to select the IEA code.
4. Click ‘Apply’ to add the new filter.

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Using the ‘Not like’ or ‘None of’ options will yield the same results.

• Using the Manage Filters feature

1. Click on the ‘Manage Filters’ button above the results table.
2. Using the ‘Add a new filter’ drop-down menu, click the GO Evidence Code field.
3. Click the blue plus sign to add your new filter, which will show a new drop-down list on the left of the GO Evidence Code field.
4. Choose the != option
5. Finally, click ‘Apply Changes’.

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Using the ‘Not like’ or ‘None of’ options will yield the same results.

How do I analyse my gene list for GO term enrichment?

Go term enrichment is calculated automatically for all gene lists. You need to navigate to the List analysis page for your list, and the GO term enrichment for your list will be displayed as a widget. For more information on the enrichment calculation, see the InterMine documentation.

Other Gene Ontology searches

HumanMine includes many other Gene Ontology related searches. To see the full range of searches, navigate to the Template Searches page and enter ‘GO’ into the search box - check Finding the template search that you want for more details.

For instance, you can find all genes in a specific organism associated with a particular Gene Ontology (GO) annotation using the GO term → Genes template. Various combinations of GO term and data searching are available; for example, Gene + GO term → Genes by GO term for a Gene or list of genes with GO annotation returns a subset of genes with that particular GO annotation.

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If you can't find what you are looking for, please Contact Us, and we can construct the template for you.