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Identification of rapidly evolving genes

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Xuping Zhou

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Nov 11, 2024, 8:37:23 AM11/11/24
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Hello everyone, 

I am working on the identification of rapidly evolving genes (REGs) and my steps are:
I ran the one-ratio branch model and two-ratio branch model, respectively.  LRT was employed to compare the one-ratio branch model to the two-ratio branch model. If a gene had an FDR-adjusted p-value < 0.05, it was considered as REGs in the foreground branch. My question is, do I need to add another condition that the foreground branch has higher dN/dS values than the background branch?

Best wishes,
Xuping

Sandra AC

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Nov 26, 2024, 4:18:13 AM11/26/24
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Hi Xuping,

Thanks for your message! If the foreground branch/es are specified a priori, based on a biological hypothesis (or various hypotheses), there is no need for FDR. If you do not have any a priori hypothesis and you have just decided to go through all the branches on the tree one by one, then there is indeed a need to correct for multiple testing. If the latter, you may use FDR to do so as you suggest -- you can also read more details about multiple testing in Anisomova and Yang 2007.

Hope this is somewhat helpful!

All the best,
Sandy
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