How to understand Upregulated and Downregulated between two conditions

Question

[georgians]

Hello All, I am a little bit confused about how to understand if any gene is upregulated between Control and Treated condition, whether it is upregulated in Control and downregulated in treated or vice versa?? What is the direction effect??

Anshul

Answer 1

[i.sudbery]

This would depend on how the test is carried out - it can be either. Usually though, people will quote upregulated as things that are higher in treatment than control, and downregulated as things that are higher in control than treatment.

[Mensur Dlakic]

Never seen it defined any other way except as you described in the second sentence. What would be the purpose in calling something a control or a baseline if the other condition was the reference point?

[i.sudbery]

My point with "it depends", was not over what is defined, but what the software actaully calculates. In fact, without being explicit, both edgeR and DESeq will often call things the other way around because factors are ordered alphabetically and C (Control) comes early in the alphabet.

Answer 2

[georgians]

Thank you for your reply!!!!