Question: How to determine Up and Down regulated genes from log2(fold change)of the Cuffdiff output?
gravatar for jiffyjohn23
4.5 years ago by
jiffyjohn2310 wrote:

Dear All I ran cuff-links/cuff-diff pipeline on my RNA-seq data. But I have some problem on how to interpret the up and down regulated genes from the cuff-diff results. I used CummeRbund for its visual interpretation.

Along with this I was trying to identify up and down genes from log2(fold-change) value generated from cuff-diff. Saw in many posts that to identify the up & down regulated genes the threshold of log2(fold change) can be set to +2 & -2 respectively and to set the significance values as < 0.05. But when we check that, those having a significance values < 0.05 are having a fold change of + or - infinity. What does that mean? How we can connect it with up and down regulation of genes?

I read all the previous posts regarding this. But I didn't get any exact concept from those posts. So please help me to clarify, how to find the up & down regulated genes. Can we consider those genes with + or - inf log2(fold change) as up/down regulated?

Thanks in Advance.

ADD COMMENTlink modified 4.5 years ago by Satyajeet Khare1.6k • written 4.5 years ago by jiffyjohn2310

Hi, I have the same issue, how did you handle it and interpreted it?

ADD REPLYlink written 4.3 years ago by bioinforesearchquestions280
gravatar for Satyajeet Khare
4.5 years ago by
Satyajeet Khare1.6k
Pune, India
Satyajeet Khare1.6k wrote:

If a gene is not expressed in one sample (zero FPKM) and is expressed in other sample, the fold change is infinite. And since it is more than 2 fold, it will be selected (provided its significant i.e. p<0.05). Threshold is lower limit. If a gene shows less than 2 fold change it will not be selected even if the change is significant (reproducible throughout the dataset, p<0.05).

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by Satyajeet Khare1.6k
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