Understanding up and down regulated genes from LOG2 foldchange or foldchange
2
28
Entering edit mode
10.4 years ago
Whoknows ▴ 960

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

protein gene-expression RNA-Seq • 305k views
ADD COMMENT
29
Entering edit mode
10.4 years ago
pld 5.1k

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.

ADD COMMENT
9
Entering edit mode
7.4 years ago
FatihSarigol ▴ 260

I really like the explanation on Wikipedia page:

In the field of genomics (and more generally in bioinformatics), fold changes are defined directly in terms of ratios. If the initial value is A and the final value B, the fold change is defined as B/A. Note that this is different to the definition described above.In other words, a change from 30 to 60 is defined as a fold-change of 2. This is also referred to as a "2-fold increase". Similarly, a change from 30 to 15 is referred to as a "2-fold decrease".In genomics, log ratios are often used for analysis and visualization of fold changes. The log2 (log with base 2) is most commonly used. For example, on a plot axis showing log2-fold-changes, an 8-fold increase will be displayed at an axis value of 3 (since 2^3 = 8).

And this paper: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

ADD COMMENT

Login before adding your answer.

Traffic: 1512 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6