Question: find significant analysis?
1
gravatar for star
2.2 years ago by
star240
Netherlands
star240 wrote:

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?

statistic fisher.test R • 400 views
ADD COMMENTlink modified 2.2 years ago by Rasoul Godini0 • written 2.2 years ago by star240
3
gravatar for arta
2.2 years ago by
arta580
Sweden
arta580 wrote:

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.

ADD COMMENTlink written 2.2 years ago by arta580

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

ADD REPLYlink written 2.2 years ago by Benn8.0k
0
gravatar for Rasoul Godini
2.2 years ago by
Rasoul Godini0 wrote:

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

ADD COMMENTlink written 2.2 years ago by Rasoul Godini0
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