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Question: Bayesian Network analysis of gene regulatory relationship
1
gravatar for nancydong20
16 days ago by
nancydong2010
nancydong2010 wrote:

Hello!

I am currently using RNA-seq to examine the roles of a few key proteins in the transcriptional response underlying a certain condition. I came across this interesting article (https://www.nature.com/articles/srep12615) where Bayesian Network Analysis (using the R package deal) was used to analyze RNA-seq data to infer which genes are acting "upstream" or "downstream" of their gene of interest. This seems really useful as it would provide me with some potential candidate genes as upstream regulators of a poorly-understood gene in the condition that I am studying, which I can test using knockdowns and etc.

I haven't come across other recent examples of this method of analyzing RNA-seq data. I am wondering if this is a methodologically sound way of identifying potentially causal regulatory relationships between genes that then can be tested using wet lab experiments?

P.S. I tried to look on Biostars for similar threads, but those don't seem to get any answers. I have also emailed the senior author of the paper, and am waiting to hear back.

Thank you very much for any light you can shed on this!

ADD COMMENTlink modified 12 days ago • written 16 days ago by nancydong2010
2
gravatar for chris86
14 days ago by
chris86320
UCL, United Kingdom
chris86320 wrote:

As far as I understand it, bayesian networks are just an alternative to correlation networks (WGCNA) or mutual information networks (ARACNE). I think your false positive rate would probably be high, but it is a valid way of finding candidates, whether it is methodologically sound.... I think that is harder to judge.

ADD COMMENTlink modified 14 days ago • written 14 days ago by chris86320
0
gravatar for nancydong20
12 days ago by
nancydong2010
nancydong2010 wrote:

Thank you very much for your input! 

ADD COMMENTlink written 12 days ago by nancydong2010
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