Question: Understanding up and down regulated genes from LOG2 foldchange or foldchange
20
Whoknows820 wrote:

Hi friends

Today i was confused with a very simple problem !! How to determine up and down regulated genes from log2 values. I would like to clear this problem:

Suppose 2 gene expression values A,B (treatment):

A=10

B=15

Foldchange is  B/A => FC=1.5 or greater is Up regulated , and if the values were B=10,A=15 we'll have FC=0.66 it means all values less than 0.66 will be down regulated.

For log2-foldchange, its formula is

log2FC=Log2(B)-Log2(A)

which then all values greater than 0.5849 were be up regulated and all values less than -0.5849 (or FC =0.666) were be down regulated genes, protein or etc.

For calculating Fold change from log2 just do , Power(2, log2_Value)
, Power(2, 0.5849)=1.5

modified 3.1 years ago by FatihSarigol160 • written 6.2 years ago by Whoknows820
20
pld4.8k wrote:

Here is a good read on how fold-changes are calculated: http://www.nature.com/ng/journal/v32/n4s/pdf/ng1032.pdf

In your case, if a 1.5 fold change is the threshold, then up regulated genes have a ratio of 0.58, and down regulated genes have a ratio of -0.58.

``````log2FC = log2(B) - log2(A)
FC = 2 ^ log2FC
``````

As it says in the linked article, log transformed fold changes are nicer to work with because the transform is symmetric for reciprocals. That means, `log2(X) = -1 * log2(1/x)`, so it is much easier to understand. Either way is equivalent, but the log transform makes it more clear.

+1 for providing the link to the review article! :)

3
FatihSarigol160 wrote: