Question: Enrichment pathways comparison between conditions
0
gravatar for judhenaosa
6 weeks ago by
judhenaosa0
Colombia/Bogot√°/Universidad Nacional de Colombia
judhenaosa0 wrote:

Hi.

I have the pathways obtained from an enrichment analysis for five conditions (Condition_A, Condition_B, Condition_C, and Condition_D). With the pathways lists, I made an intersection set (vennDiagram), and I obtained the number of common pathways for every possible combination just the next table shows:

Comparison Common_path_Number
Condition_A vs Condition_B vs Condition_C vs Condition_D vs Condition_E 13
Condition_B vs Condition_C vs Condition_D vs Condition_E 1
Condition_A vs Condition_C vs Condition_D vs Condition_E 1
Condition_C vs Condition_D vs Condition_E 2
Condition_A vs Condition_B vs Condition_D vs Condition_E 0
Condition_B vs Condition_D vs Condition_E 0
Condition_A vs Condition_D vs Condition_E 1
Condition_D vs Condition_E 3
Condition_A vs Condition_B vs Condition_C vs Condition_E 0
Condition_B vs Condition_C vs Condition_E 0
Condition_A vs Condition_C vs Condition_E 0
Condition_C vs Condition_E 0
Condition_A vs Condition_B vs Condition_E 0
Condition_B vs Condition_E 0
Condition_A vs Condition_E 3
Condition_E 4
Condition_A vs Condition_B vs Condition_C vs Condition_D 20
Condition_B vs Condition_C vs Condition_D 3
Condition_A vs Condition_C vs Condition_D 4
Condition_C vs Condition_D 9
Condition_A vs Condition_B vs Condition_D 0
Condition_B vs Condition_D 0
Condition_A vs Condition_D 0
Condition_D 18
Condition_A vs Condition_B vs Condition_C 3
Condition_B vs Condition_C 1
Condition_A vs Condition_C 0
Condition_C 12
Condition_A vs Condition_B 1
Condition_B 2
Condition_A 3

Now, I need to establish if they are significantly intersected. I guess the best way is using a Fisher test. If so, What is the correct form to create the contingency table?

If you have any tips to resolve this task. I will appreciate it.

Kind regards,

Juan

ADD COMMENTlink modified 4 weeks ago by egeulgen960 • written 6 weeks ago by judhenaosa0
0
gravatar for egeulgen
4 weeks ago by
egeulgen960
Istanbul
egeulgen960 wrote:

Initially, I thought you could try a multivariate hypergeometric distribution based test, implemented as MultiHypergeometric in the CRAN package extraDistr.

After searching a while, however, this article also looks very promising:

... developed a theoretical framework for computing the statistical distributions of multi-set intersections based upon combinatorial theory, and then accordingly designed a procedure to efficiently calculate the exact probabilities of multi-set intersections.

Bonus:

We further developed multiple efficient and scalable techniques to visualize multi-set intersections and the corresponding intersection statistics.

The method is available as an R package: SuperExactTest

Hope this helps, -E

ADD COMMENTlink written 4 weeks ago by egeulgen960
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