Question: Pathway analysis for two lists of genes
1
gravatar for Na Sed
5.4 years ago by
Na Sed310
United States
Na Sed310 wrote:

I have 2 gene lists with 13 members, called A and B. The list A, includes main genes which I am sure about their functionalities, whereas the list B includes genes which I aim to study them.

I would like to do pathway analysis for list B to find how much the list B is similar to list A. So, I developed two approaches but I am not sure if they are correct and meaningful. Hence, I decided to write them here to know your opinion about them and get help from you guys.

First Approach:

1) Do pathway enrichment analysis  for each list of genes distinctly as follows:

for list X and pathway Y, we determine:

a = the number of common genes between list X and pathway Y
b = the number of genes in pathway Y
c = The number of genes in whole pathways - b
d = the number of genes in list X

p-value = dhyper(a, b, c, d)

2) For each list A and B, find pathways with p-value < 0.05, called pathway_A and pathway_B.

3) Find the common pathways between pathway_A and pathway_B.

Finally, the list B is functionally related to list A, if there is a common pathway in step (3).


Second approach:

1) Find pathways which include some genes from list A, called pathway_A.

2) Find pathways which include some genes from list B, called pathway_B. 

3) Find common pathways between pathway_A and pathway_B, called pathway_AB.

4) For each pathways in pathway_AB,

4-1) repeat the below instructions for 100 times:

4-1-1) Select 13 genes randomly from all genes in all pathways, called randGenes.

4-1-2) Find pathways which include some genes from randGenes, called randPathway.

4-2) Find the number of times which the interested pathway, selected in step (4), is included in randPathway, called n_rand.

4-3) p-value = n_rand/100. 

We do step (4-1) to (4-3) for all pathways in pathway_AB, so we get p-value for each of them. Finally, the list B is functionally related to list A, if there is a pathway with p-value <  0.05.

 

Thank you!

R gene pathway • 2.0k views
ADD COMMENTlink modified 3.3 years ago by Biostar ♦♦ 20 • written 5.4 years ago by Na Sed310

Why do you only have 13 genes to start with for each A and B? Secondly, you don't seem account for genes which take place in more than one pathway, or have overlap.

ADD REPLYlink written 3.3 years ago by theobroma221.1k

Just to follow up, here is a good paper which addresses crosstalk, or the overlap I spoke to above: http://m.genome.cshlp.org/content/23/11/1885.short

ADD REPLYlink written 3.3 years ago by theobroma221.1k
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