How to determine Up and Down regulated genes from log2(fold change)of the Cuffdiff output?

Question

[jiffyjohn23]

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.

[bioinforesearchquestions]

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

Answer 1

[Satyajeet Khare]

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).