Calculation of Observed.Target.Gene.Overlap.Proportio

[ralodo93]

We were trying to understand how do you calculate the Observed.Target.Gene.Overlap.Proportio by doing the operations by hand.
Let me provide a concrete term example:

This is our results:

GO.term.ID GO.term.size Observed.Target.Gene.Overlap.Proportio Mean.Random.Simulated.MicroRNA.Target.Overlap.Proportion
hsa03010~Ribosome           27                             0.00276243                                               0.00445511
   One.sided.empirical.p.value Benjamini.Hochberg.0.05.FDR
                   0.345034                           -

This is involved-genes.txt

>hsa03010
MIR1	
MIR2	GEN1,GEN2
MIR3	
MIR4
MIR5	
MIR6	
MIR7	
MIR8	
MIR9	
MIR10

What we are expecting is
Observed.Target.Gene.Overlap.Proportio = 2 / 27
Being 2 (GEN1,GEN2) the number of target genes and 27 the number of genes annotated in hsa03010.
But 2/27 (0.07407407) is not the reported Observed.Target.Gene.Overlap.Proportio (0.00276243).

[zagganas]

As specified by Bleazard et al., the overlap proportion is the number of the group's targets targets participating in the process divided by the total number of the targets. This means that in your case, it would be 2/n where n is the union of genes targeted by MIR1-MIR10.

[zagganas]

Also n=2/0.00276243 which is about 724 genes.