Following the advice from an old threat in Bioconductor I found with metabolic pathways are targeted by my miRNA. Now I would like to understand what does it mean that a group of miRNAs target certain metabolic pathways (in the biological sense).
Following the cited protocol I end with a list of duplicated KEGG pathways. I have 5 allegedly interesting groups of miRNAs. However for each group of miRNAs the number of targeted pathways is different.
The originally miRNA groups are formed by 263, 104, 115, 515, 44 different miRNAs (in total 1041)
Each group targets 5971, 6355, 7438, 1410, 5594 pathways
However only 224, 222, 226, 184, 218 pathways are unique for each group
The universe (all the miRNA of all groups) targets 9322 pathways which 227 are unique
To understand if the groups of miRNA are randomly targeting or not I thought to perform a hypergeomtric test, comparing each group with the universe of targets. (Although I am not sure if a hypergeometric test is the right choice, or how to do it)
To see if they target the same metabolic pathways in the same frequency I could compare the targets between the different groups. Both the absolute numbers of unique pathways as well as the frequency in which each pathway is targeted in each group.
In order to see the relative participation of each group I could also compare for each group how much a metabolic pathway has been targeted compared to the universe of targets.
Is there any approach better than others? Should I do any other analysis I have forget?
