Observed percent co-expression sign. higher than random samples

[Nicholas Price]

Hi,

I have a set of Arabidopsis genes that I want to test whether they show significantly higher linkage through co-expression than 1000 random samples (sample size:157 genes)? (note: these genes were chosen independently of any expression data). 

Is it possible to do such analysis using GeneMania  or is there another more suitable tool? 

Best

Nicholas

[Gary Bader]

Hi Nicholas - not automatically. GeneMANIA does have co-expression networks, also available for download, but it doesn’t compare to random samples. STRING has a p-value for its networks, though you may not have fine control over the networks that are used. Best would likely be for you to script the random sampling yourself.

Best,
Gary

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[Nicholas Price]

Hi Gary,

Yes, I will generate random samples.

So I guess I will download the networks to examine the random samples. 

Thank you

Nicholas

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“It is easy to invent a selectionist explanation for almost any specific observation; proving is another story”  Motoo Kimura.