Hello Akiko! That's a good question. Well, it actually depends on the kind of the desired result you are expecting at the end. But, in general, it mostly works well if you do separate ontology analyses for the upregulated and downregulated genes. In that way, you will be able to find out the probable functional categories in your upregulated and downregulated genes separately. I think if you are doing a combined ontology for all the differentially expressed genes then at the end, you might run into certain awkward problems because then it becomes really hard to discern whether the categories are coming from the upregulated or downregulated genes.

Hi Akiko

every pathways you can look for contains down and up regulation mecanims for normal procedures in cells. Testing therefore up and down regulated genes could have a sense and lead to an answer of the disease or mecanims you're studying. the perfect illustration is cancer, for which you have oncogenes and also anticancer genes, alternatively down or upregulated in all times, even in pathologies (in addition to the mutational status of these genes and their copy number...).

stay safe

fred

Frederic Lepretre

Hi Frederic

Merci beaucoup pour votre bonne réponse ;)

I think that gene expression of many genes is not independent and affected each other, so it makes sense to me to use all differentially expressed genes (both up- and down-regulated genes simultaneously) for ontology analysis. In addition, I believe that the algorisms used for DAVID and clusterProfiler are designed for using all differentially expressed genes (Am I correct?). I wanted to know the opinions by bioinformaticians.

I also wanted to know the reasons why only up- or down-regulated genes were used for ontology analysis in some studies, which I suppose that there must be particular reasons.

Merci, et reste en bonne santé ;)

Akiko

c'est un plaisir

un grand bonjour au Japon

fred