Skip to main content

NCBI Resources: GEO2R

Contains information about the NCBI databases to be used as a teaching tool.

GEO2R

GEO2R is useful for taking a quick look at uncurated datasets in GEO. You can:

  • See the Top250 expressed genes
  • Look at quality control data
  • See a profiles graph
  • Export an R script

See the tutorial below to learn how

Need help? Ask Wlad

Search for series accession

Step 1: find the GEO series you want to analyze. Enter the GSE (series accession number) into the search box and hit "set".

Assign Groups

Because the data are not curated, GEO2R doesn't know which samples are in the treatment and control groups. So, you have to tell it. To do this, click Define group and name one of the groups. In this example, there are 3 groups HSPC, EPP, and MPP with 3 replicates each. After naming the groups, they will appear in the Define Groups dropdown.

Then, select the samples you want to put into the first group. Then click on the group you want to assign them to by clicking on that group. They will change color to correspond with the group.

Repeat this for all groups, and it should look something like this:

 

 

Top250

After hitting the top250 button, you should see output that looks like this. Each row of the table represents a probe on the gene array. Each column represents an attribute about the data from this probe (P-values, F statistic, Gene Symbol and Title). If you click the carrat to the left of the probe ID, you can see an expression profile graph for that probe in each sample type.

Value Distribution

Click on the value distribution tab, and click View. You will see a box plot for each sample. This option lets you assess variability across the samples.

Profile Graph

But what if you want to see an expression graph for a gene that's not in the top 250? You can use the profile graph too. The complicated piece if this is that you cannot search by gene name, you must search by probe ID. Luckily there is a link to the plat form record on this page. Find your gene of interest (if available) in the platform, and find the corresponding probe name to search. 

Example: ILMN_1343295 is the probe name for the GAPDH gene.