Question: How to determine Up and Down regulated genes from log2(fold change)of the Cuffdiff output?
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gravatar for jiffyjohn23
3.3 years ago by
India
jiffyjohn230 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 3.3 years ago by Satyajeet Khare1.5k • written 3.3 years ago by jiffyjohn230

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

ADD REPLYlink written 3.1 years ago by bioinforesearchquestions270
2
gravatar for Satyajeet Khare
3.3 years ago by
Satyajeet Khare1.5k
Pune, India
Satyajeet Khare1.5k 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 3.3 years ago • written 3.3 years ago by Satyajeet Khare1.5k
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