GFOLD value cutoff

Question

[Kurban]

Dear all,

I have two groups of RNA-seq data, one of them are for treated sample and another one is for control. Unfortunately they are without any replicates (I know experimental design without any biological replicate is not a good thing). so I have used GFOLD calculated GFOLD value for each transcripts. then I ranked the value got more than 5900 transcripts (GFOLD value>1) out of more than 56000 assembled sequences. here I wanna set a cutoff for following enrichment analysis, but I do not know how to set a reasonable one, could you give me some suggestions?

Answer 1

[jianxing.tongji]

There is no gold standard cutoff. To understand this, just consider gfold as a reliable log2 fold change. The only thing hold is that large absolute gfold value corresponds to large express changes.For enrichment analysis, just take the top genes, 1000, 500, 2000, etc. The biological conclusion should be consistent.

[biolab]

Hi, Jianxing, I have a further question. Kurban set GFOLD value > 1. That will select up-regulated genes. Then how to set GFOLD value to select down-regulated genes using the same criteria as selecting up-regulated genes? Is it GFOLD value < -1? Thank you very much!

[jianxing.tongji]

The GFOLD values are symmetric around 0. For up-regulated genes, you can take GFOLD>x and for down-regulated ones, you can take GFOLD<-x.

[biolab]

Thank you very much. It's much helpful.