BioGPS

Go to parent Basic bioinformatics concepts, databases and tools#Exercises_during_the_training

Go to BioGPS. BioGPS tries to collect all relevant information that is available for genes of a number of model organisms (see slides for list of organisms). The basic building blocks of BioGPS are genes. So the most obvious search you can do on BioGPS is a search on your favourite gene. For all genes in BioGPS they gathered the most commonly used IDs (Gene symbol, Entrez Gene ID, Ensembl ID, Affymetrix ID, InterPro ID ...) so you can use either one of these identifiers. When you submit an ID of your favourite gene you are redirected to its Gene report. You can enter the ID of one gene or you can enter a list of IDs of multiple genes. In the latter case you will be redirected to a summary page containing the search results for all the genes.

After a search, the default layout of the Gene report is shown containing a concise overview of the info about your favourite gene. It consists of three sections belonging to three different plugins.

• On the right you see a list of all identifiers of the gene with links to the source databases. You can select to view these identifiers for different organisms.
• On the left you see gene expression info. By default you see Human Gene Atlas data but you can change to other data sets. The Human Gene Atlas shows the expression patterns of the gene in different anatomic regions
• At the bottom you see the Gene wiki entry

You can change the default layout to a number of other layout to access different types of information, e.g.

• The Model Organism Databases layout takes you to a page with direct links to model organism databases like Mouse Genome Informatics or the Rat Genome Database. There you can see for instance if mouse knockouts for your gene are available.
• The Literature layout performs a Pubmed search for your gene of interest.
• The Reagents layout takes you to a list of suppliers (e.g. Sima Aldrich, Applied Biosystems...) to see which reagents are available for your gene of interest.

Exercise 1: search for TTR

Retrieve the gene report for TTR (transthyretin).
In the search box type TTR and click Search by symbol or accession

BioGPS finds three hits (the second hit is from another gene with the same symbol).
Click on the first hit to retrieve the Gene report.

For which species will BioGPS provide info of this gene ?
You can see that for BIOGPS contains info on TTR in all supported organisms except Arabidopsis.

Which human organ shows the highest expression of TTR ?
When you scroll through the gene expression section, you see that the highest expression of TTR occurs in liver.

Which mouse organ shows the highest expression of TTR ?
In the gene expression section set the Species to M. musculus (mouse) and scroll through the expression section. You see that also in mouse, expression of TTR is highest in hippocampus and liver.

According to the gene wiki TTR has a beneficial effect on Alzheimer's disease by binding to which protein ?
In the bottom window the gene wiki is shown by default. When you scroll down the page to the Role in disease section. There you see that "TTR is also thought to have beneficial side effects, by binding to the infamous beta-amyloid protein, thereby preventing beta-amyloid's natural tendency to accumulate into the plaques associated with the early stages of Alzheimer's Disease3.

We are going to cross check if TTR binds to beta amyloid by loading in data from the STRING database, a database of protein-protein interactions.

Which proteins interact with TTR ?

At the top of the Gene report, click Plugins You are redirected to the BioGPS Plugins library. In the Most popular section, click STRING - Proteins and their Interactions Click Add to Layout This opens the plugin as an additional section in BioGPS. If you want to have a clearer view on the interaction data you can click the More options button and select Open in browser. You see a graphical representation of the interactions between TTR and its interaction partners. When you scroll down you see a table containing a description of the type of data/information that led to the prediction of these proteins as interaction partners of TTR and a score representing how sure STRING is of these predictions. Both in the graph and in the table you see that TTR indeed interacts with APP, beta amyloid.

When you click the dot representing experimental evidence in the table you are redirected to a page where you actually see the evidence (= publication).

What kind of experiment was used to identify the interaction of TTR and APP ?
At the top of the page you see that the interaction was identified by a coimmunoprecipitation assay.

Is this interaction also known in mouse ?
At the top of the String window in BioGPS switch Species:HS to Species Mm. Also in mouse TTR and APP are known to interact.