find significant analysis?

Question

[star]

I have done Differential expression (DE) analysis and found 2212 DE genes in my data, then I found the overlap between my DE genes and some diseases related genes (e.g. ALS). ALS disease contains 1007 genes that 500 of those had overlap with DE genes. Now I would like to find these number are significant or not?

Answer 1

[arta]

You can use hypergeometric test which is similar to fisher test and in the following link you can find an example about how to do that.

[Benn]

There is also an R package especially for this purpose, geneOverlap.

Answer 2

[Rasoul Godini]

Hi To find significancy you need an statistical threshold like p-value. to make that you need some repeats. But in here you have only genes selected by a threshold already. Here, you can use Venn diagram to show common DEGs and punctuate on findings by writing about percentage of your DEGs which are common with disease specific genes. Good Luck