Statistical test for target enrichment for each microRNA

Question

[Amaranta Remedios]

Hi, I have this conceptual question that I have been struggling with for a while due to my poor knowledge of statistics. I hope someone can help me to identify the correct test.

I have a list of microRNAs in a specie, and I have predicted the targets for each microRNAs. I have also done differential expression analysis so I know how much each target (mRNAs) is expressed (log2Fold) at any given point.

So let's say I got this info for each miR in a dataframe:

microRNA    Total_genes Total_Targets   Targets_in_t1   up_t1   down_t1     nosig_t1
bantam-3p    61064      1918             544              47      60           437

Where Total_genes is how many UTRs I used for the target prediction. Total_targets is the total mRNAs that each microRNA could target and Targets_in_t1 is how many targets where present for each microRNA in timepoint 1.

How could I statistically determine if the targets for bantam are enriched at time point 1 ( I got 544 targets out of 1918 possible ones, and of these 544, 47 were unregulated, 60 down regulated and 437 non significantly regulated).

I have been trying to do hypergeometric test but couldn't get my head around the numbers. I have also tried to do a t-test but I'm reluctant to it, it seems too basic my go to place due to ignorance.

Anyway, thanks and hope someone can help!

[Papyrus]

Hi, it was a bit difficult (at least for me) to follow your description. Can you confirm if you did this?:

• analyze the expression of 61064 mRNAs
• of those 61064, a total of 1918 are classified as bantam targets
• in your expression analysis, you got 544 mRNAs out of the 61064 (some are bantam targets, some are not)
• of the 544 significant mRNAs, 47 (up) and 60 (down) are classified bantam targets