microRNA target finding : 3p vs 5p?

Question

[illinois.ks]

Hello all,

I have found differentially expressed microRNAs. And I would like to see the target genes of them. (mouse species)

I have searched several dbs. and downloaded predicted dbs (e.g. mirDB5.0 and targetscan and MIRANDA)

I have two questions.

1. Which DB is better? Any preference? Or use union of all?
2. For mirDB case, It has annotated mmu-mir-34a-3p and mmu-mir-34a-5p. In order to find the target genes of mmu-mir-34a, which one I have to use, mmu-mir-34a-3p VS mmu-mir-34a-5p? It seems they have different targets.

Any suggestions?

Answer 1

[Asaf]

They have different targets because they have different sequences, they are the two sides of the pre-miRNA stem-loop. Try to see in your data which side is expressed (if you have the sequences of mature miRNA) or literature.

[illinois.ks]

Thank you!

Then, how about targetscan? Miranda? In this DB, miRNAs and targets relationships are just annotated without 3p or 5p. Then how can we map the mirna target relationship? If I want find a targets of a list of mirnas(without 3p ,5p), then can I use targetscan/ miranda?

[Asaf]

Historically, the 5p was the miRNA and the 3p was the miRNA*, it chenged to 5p and 3p in some databases along the years. As you can see here: http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0000584 the 5p is the major one and is probably the only active one in this pair.

[illinois.ks]

Thank you for your explanation. So, Then is it the common for all miRNAs? (e.g. 5p was the major one? Or it depends on miRNAs? Then, Every time Do I have to check it?) I have used edgeR to identify DE miRNAs. So, I just got the list of miRNA names. (e.g. mir-320, mir-32.. and fold change ratio. no information regarding to the 3p/5p.) I just would like to find target genes for each of DE miRNAs.

[Asaf]

If you got this list, someone mapped the reads to the genome and counted how many reads each miRNA has, he or she should have this information. And yes, it's common to all miRNAs.

[illinois.ks]

Thanks you so much!! I see .. I did the mapping using bowtie2. So, I need to check the bam file to see the real sequences. then.. to see whether identified miRNA is 3p or 5p or not ! :)

miRNA seems much more complicated then mRNA... since I have to check all DE miRNA real mapped sequences... ;P

[Asaf]

It's more complicated in a lot of ways, e.g. mapping to the correct miRNA (if you have mature miRNAs) in a family, separating mature and pre/pri-miRNAs. My guess is that you sequenced the pre-miRNAs so mapping would be easy but you wouldn't be able to tell which one is the active one.

[illinois.ks]

I am trying to see the read sequences mapped to the miRNA. (e.g. mir-340) to see whether it is mir-340-5p or mir-340-3p. But I don't know how I can see this..

Could you please let me know?

[Asaf]

You can try and upload your bam file to IGV or other browser and browse to the miRNA gene, you will be able to see the coverage in that region either it's specific to either 5p or 3p/pre-miRNA/pri-miRNA

Answer 2

[Inbalor]

How you get the differentially expressed miRNAs? If it is by sequencing you should have to have the sequence. Then, you can look for it in miRBAse and check which arm is coming from. I would strongly recommend to do not base your target predictions in only one method. Use at least two of them and consider only those targets that come up using both methods. This is because the high positive false results that you obtain from the target prediction algorithms.

[illinois.ks]

I got the differentially expressed miRNAs from NGS data. I have used bowtie2 and edgeR to identify DE miRNAs.

Since, in this case, I only got the list of miRNA names and I don't have real sequences.. bowtie2 did the mapping.. Hm... Then, how can I do it?

Bowtie2/htseq-count/EdgeR

In this procedure, I only got the name of miRNAs without 3p or 5p.. :(

Which part do I have to go back to check the 3p or 5p info?

[nikhilvgbt]

Hello, illinois.ks... how did you do this analysis, as i have got the miRNA from NGS data, I only got the list of miRNA names and I don't have real sequences, e.g MIR34, MIR211 etc and i wanted to find target ,,,, should i consider both 3p or 5p for MIR34 ??..