GEO2R provides many graphs and a complicated-looking table. In this lesson, you'll learn what they mean.
At this point, your screen should look like this.
Let's take a look at the results.
This table shows the top 250 differentially expressed genes by p-value. This means that it ranks the genes by how confident we are that the gene is different between people with Covid-19 and people without.
The P Value column is for statistical significance. You want to only consider genes that have P value of less than 0.05. This means that you are 95% confident that the gene is statistically significantly differentially expressed.
The logFC column is also important. FC stands for fold change and is a ratio of the expression of the gene in COVID-19 patients vs. controls. A greater fold change means there is a bigger difference. Note that it is LOG FC, meaning that the value in the table is the log 2 version of the actual fold change.
For example, if a given gene is 16 times more expressed in COVID-19 than healthy people, the logFC would be 4 since 2^4 = 16.
The SEQUENCE column gives you the sequence of the gene and the ORF is the gene name.
If you click on a row of the resulting table, a graph will appear. The graph shows the expression of that gene in each patient sample. As you can see in this example, all of the COVID-19 patients have higher expression of gene TEX101 than controls.
Click on Download full table if you want to download the whole data table for further analysis (not covered in this course). This full data table will contain the results for all the thousands of measured genes, not just the top 250 most differentially expressed ones.