🛣️Pathway Enrichment

How to run pathway enrichment analysis on the genes returned in you graph model report.

The enrichment analysis identifies if the input set of genes from the report significantly overlaps with annotated gene sets and pathways.

In order to run a pathway enrichment, the unbiased concept used within the report must contain Genes

Step 1: Create a graph model where one of your concepts contains genes. Detailed instructions on how to do this can be found here.

Step 2: Create a report using the model where the unbiased concept is "Gene".

Step 3: Open the report and select the "Pathway Enrichment" tab.

By default the first 1500 genes returned in the report will be used for the pathway enrichment. To adjust this number select "filter" and you can update the total number of genes included in the pathway enrichment. For example setting the start to 0 and end to 100 will include the first 100 genes. Use the database input to select from numerous databases. Click on a pathway to view the genes from your report that are involved in the selected pathway.