Question: What is the interpretation of the obtained p-value here?
0
gravatar for Na Sed
4.7 years ago by
Na Sed280
United States
Na Sed280 wrote:

I am doing Over-Representation pathway analysis as described here

In this way, the p-value is calculated for each pathway as follows:

where N is the total gene number on all pathways. K is the gene number on a certain pathway. M is the number of genes of interest. x is the number of genes hit on this pathway.

Assume, we have 56340 genes on all pathways (N=56340), the number of genes of interest is 1 (M=1), and the number of genes in given pathway is 30 (K=30). Moreover, none of genes of interest hit the pathway, so x=0.

If we calculate p-value, we get

p =1- dhyper (0, 30, 56340-30, 1) = 0.0005324814

(Please note it is less than 0.01.)

After calculating the p-values for all of pathways, I obtain many p-values less than 0.01.

Now my question is: how can I choose enriched pathways based on the obtained p-values? As you can see when none of genes of interest hit the given pathway, we obtain p-value less than 0.01, as well. Is it rational if I consider pathways without any common gene with genes of interest as enriched pathway?

Can anyone help me?

Thanks

ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by Na Sed280
1

For enriched pathways, you'd just look at a one-tailed probability...
 

ADD REPLYlink written 4.7 years ago by Devon Ryan94k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 731 users visited in the last hour