A tutorial for target prioritization

Identify the enriched biological themes

8. At the lower part of the list analysis page, you can find several enrichment widgets. Let’s start from the ‘Pathway Enrichment’ widget.

9. Change the ‘Test Correction’ to ‘Benjamini Hochberg’, which is a less strict multiple testing error correction method.

10. In this example, we only want to use KEGG pathway. Thus, change the ‘DataSet’ to ‘KEGG pathways data Set’.

11. Check the checkbox beside the top 10 enriched pathways (which has the least p-values).

Select enriched pathways

Select top 10 enriched KEGG pathways and save the associated genes in a new list

12. Click the ‘View’ button above the table, then click ‘Create list’ button.

Create a list from enriched pathway

Create a new list from enriched pathways.

13. You will see a pop-up windows. Enter ‘Top 10 KEGG’ as the name and click ‘Create’ button. The genes in the list which associated with the top 10 enriched KEGG pathways will be saved as a new list named ‘Top 10 KEGG’.

Name the new list

Name the list as ‘Top 10 KEGG’ and save it.

14. Do the same operations for GO and DO to get 2 more gene lists. If you have no idea, here are descriptions for the operations.

  • In the Gene Ontology Enrichment widget, choose ‘Benjamini Hochberg’ for the ‘Test Correction’ and ‘biological_process’ for the ‘DataSet’. Select the top 10 enriched GO terms, click the ‘View’ button then click ‘Create list’. Name the list as ‘Top 10 GOBP’ and click ‘Create’ to create a list.
  • In the Disease Ontology Enrichment widget, choose ‘Benjamini Hochberg’ for the ‘Test Correction’. Select the top 10 enriched DO terms, click the ‘View’ button then click ‘Create list’. Name the list as ‘Top 10 DO’ and click ‘Create’ to create the list.
Select enricehd GO and DO terms

Do the same operations for Gene Ontology and Disease Ontology

15. Then you will get 3 new lists.

Three new lists

You can see the information at the top of the page.