Question: Is there any established fold-change threshold for miRNA microarray data?
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gravatar for Joe_daisy
3.8 years ago by
Joe_daisy20
China
Joe_daisy20 wrote:

I am analyzing miRNA microarray data and I would like to establish a fold-change threshold which is biologically significant. Classically for mRNA microarray a 2-fold-change cutoff was used, but I think that if we use that for miRNA as well, were could be loosing some information given that miRNA regulate gene expression. In other words, which is the miRNA expression level change, in which we could see an effect in mRNA expression? 1.5-fold change would be enough? I am asking this because in general, the fold-changes I see in the literature are not very big.
I have seen some papers not using any filtering criteria and others use 2-fold change cutoff. Is there any paper where has been studied this issue? I haven't found anything but there may be some.

Thank you,

mirna expression • 2.1k views
ADD COMMENTlink modified 2.9 years ago by Jean-Karim Heriche18k • written 3.8 years ago by Joe_daisy20

I'm also very curious about it. It seems that microRNAs degrade only small amount of mRNAs (fine-tuning), but sometimes they reduce significant amount of mRNA like transcription factor. I want to find some answers for this question T^T

ADD REPLYlink written 2.9 years ago by ysora900
2
gravatar for Jean-Karim Heriche
2.9 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

There's no definite answer. Depending on the process and genes one is looking at a small change can be biologically relevant whereas in another context, only a large change would have a significant biological effect. The 2-fold cutoff used is arbitrary. You could start with ranking your genes based on fold change and see if there's anything interesting towards the top and bottom. If you plot the ordered fold changes, there may be an elbow in the plot at one or both ends suggestive of cutoff values.

ADD COMMENTlink written 2.9 years ago by Jean-Karim Heriche18k
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