# GO Tutorial: Annotating A Paper

## Exercise IV

### Annotation

This exercise gives you a taste of manual annotation, culminating in reading a paper and annotating a protein. Working through the following tutorial should help you get a grasp on the tools available to annotators. It is based on the Gene Ontology Annotation (GOA) Tutorial by Evelyn Camon.

### Searching and Browsing GO

There are a number of tools available for navigating and searching the gene ontologies and their associated genes or gene products. The two main browsers are AmiGO and QuickGO. AmiGO was developed by the GO consortium and allows you to search the GO database for both terms and for gene product annotations. It uses annotations made by all the contributing databases and is updated monthly. QuickGO was developed at the EBI and only holds GOA annotation data, but is updated more frequently.

Try searching for "glucose metabolism" in AmiGO and in QuickGO. Note how the data displayed by the two browsers differs. QuickGO also has the useful feature of showing terms that are commonly annotated with the search term. This can help suggest other GO terms that may be relevant.

Using either browser, find the name of the GO term with the synonym "sec61 complex".

What terms are often annotated with amino acid biosynthesis?

Clicking on the children and the parent terms allows you to navigate the ontologies. Both browsers allow you to view the terms as a graph or as a denormalized tree, with one line for each GO term.

AmiGO lists the gene products which have been annotated to that term or to its children. You can use AmiGO to search for a GO term and view the gene products annotated to it, or to search for a gene product and view the GO terms it has been assigned.

What terms have been annotated to the gene product "Buffy"? What species is the gene product from?

The same information is also available in DAG-Edit. Get the full GO file and load it up using the OBO flat file adapter. Highlight the term you are interested in and select the Gene Product item from the Plugins menu. A new window will appear, showing the number of gene products annotated to the term. From this window you can select a gene product and view the terms it has been annotated to or open an AmiGO window showing the information.

Use the DAG-Edit search tool to find the term "allene oxide synthase activity ; GO:0009978". One gene product has been assigned to this function. What is it and what process is this gene product involved in?

The paper you will be reading later concerns a protein with the SwissProt accession number Q8TDE4. Using the QuickGO browser, can you find out what terms has it already been assigned?

### Annotating

You should read the GO consortium annotation guidelines before starting any annotation. The important point to remember is that GO is interested in the normal activity of a gene product: where it acts, what its functions are and what processes it contributes towards.

When you have isolated an informative phrase or word in some text, look it up in a GO browser and find the corresponding GO ID. In some cases, the term used in a paper may not be the name used by the GO term, so it can be helpful to search the synonyms and definitions of a term, or to search for a key word.

For example: I have a gene product involved in the synthesis of glucose. What GO term should I use?

You may find that viewing a pared-down GO ontology (GO slim) will give you an idea of the kind of terms that GO covers. Load it into DAG-Edit (use the OBO flat file adapter as usual) to view the terms. Unfortunately this file is now quite out of date - you may be able to spot some erroneous relationships!

Here are two text snippets; read them and try to pick out some GO terms which describe the gene products. Use one of the GO browsers to search for GO term IDs; you may find QuickGO browser more helpful as it has more comprehensive search options.

"Mutants with defects in RNA binding protein (RBP) are defective in cell growth and differentiation. An example RBP that regulates development is provided by the Bruno protein and its role as a translational repressor of oskar mRNA. In Drosophila, oskar is required for formation of germ cells and positioning of the posterior of the embryo."

[Ignore the fact that this text mentions proteins in more than one species]

From the following text, what GO terms would you assign to RERG?

"Using microarray analysis, we identified RERG (ras-related and estrogen-regulated growth inhibitor). Like Ras, RERG protein exhibited intrinsic GDP/GTP binding and GTP hydrolysis activity. Unlike Ras proteins, RERG lacks a known recognition site for COOH-terminal prenylation and was localized primarily in the cytoplasm."

Check your answers.

Now read the paper "The PGC-1-related Protein PERC Is a Selective Coactivator of Estrogen Receptor alpha." by Kressler et al. and work out what GO terms you might use to annotate PGC-1-related estrogen receptor alpha coactivator. It will help to keep a note of key phrases and the GO terms associated with them.

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