This weeks bioinformatics bite will answer a question from the end of last week’s post:
What is the expression of ITGA2 gene in prostate cancer cells?
I’d check GEO profiles, because it is a gene centric question. Let’s start by typing in prostate cancer in the GEO profiles search box.
Note the link back to the GEO data set that this gene profile was derived from (green circle). You can also see the platform and the specific probe that measures this gene (orange box). Finally, you can see a cartoon of the expression level between sample and control on the right side of the record.
To narrow down your search to a specific gene, use the filters on the left to select an organism (red box) and a Gene symbol (blue box, make sure to check that you’re using the correct gene symbol). Let’s look for the ITGA2 gene in human derived samples.
After applying the filters (blue and red boxes), you can see the search strategy in the Search details (orange box).
To get a close up of the expression graph, click the cartoon on the right (green circle).
At a glance, you can see that ITGA2 expression goes up when the microarray miR-205 is expressed (red bars). It also indicates how highly this gene is expressed relative to other genes from the same sample by percentile (blue squares). It also lists the expression values from each sample in a table below, along with its rank.
If you need more information about how the samples were prepared, you can click on the GSM number in the table. From there, you can access general information about the experiment by clicking on the Series ID (GSE) on any sample page, or the original GEO profile record.
But what do you do if the gene you’re attempting to access data in an uncurated data set? NCBI has a tool for that: GEO2R. We will discuss how to use this tool next time.
- C. Tobin Magle, PhD, Biomedical Science Research Support Specialist