To do pathway over-representation analysis (ORA) you first need to upload a
list of gene identifiers and associated fold-change in gene expression
values (and P values) as described here.
You have two options to do so:
If you have multiple probes for the same gene these values will be averaged for the purposes of the pathway ORA.
A list of pathways associated with the uploaded genes will be returned.
To do the pathway ORA click on the red Pathway ORA button at the top of the page.
This will take you to a page where you can choose the parameters for the pathway over-representation analysis.
First you need to specify whether you are analyzing an entire array dataset or just a subset of genes. If you try to analyze a subset of genes using the entire dataset algorithm or vice versa your results will NOT be correct. If you are analyzing a complete array dataset choose the following parameters for the pathway over-representation analysis:
Now choose the analysis algorithm and multiple testing correction method:
A new page will be returned showing the pathways that are significantly associated with up-regulated genes.
Click the green button to see pathways that are significantly associated with down-regulated genes.
Click on the 'summary' link to see information for all genes in the pathway. The interactions in the pathway, along with overlaid gene expression data can be visualized by clicking on the 'visualize' link.