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Over-Representation Analyses (ORA)

We know the differentially expressed genes that can be interpreted as "marker" genes for each clusters, but sometimes we need the help of databases to make sense out of our gene sets ! We propose to investigate with a first method called "Over-Representation Analysis" and you can learn more about ORA in the reference manual.

Do it yourself!

Render your RMD/QMD

To complete this week you'll need to :

  • 1. For both database : Gene Ontology and KEGG :
  • a. Describe in your own words the database
  • b. Perform the ORA based on the database
  • c. Visualise the result (top 5 per ontology class or top 15 KEGG category), Describe the plots
  • d. Create a dataframe with all results for every cluster
  • e. How many gene sets are significantly associated with each cluster ?

IMPORTANT

Please note you must be explicative in your cutoff choices and provide detailed explanations for each step of your thought process In general, try to explain in your own words for each step of your analysis!

Add your RMD/QMD in your Trello card. You can also add the html version of your rapport.

Thank you for your attention and see you next week 👏 👏 👏