Dear Maryam,

I understand the desire to have a database, check it out and get a good idea what your microRNA of interest is doing. In my opinion such an universal database does not exist and the ones that exist are most likely of mixed to poor quality. This may sound harsh and ignorant but such databases will compile data from the literature, and the publications on microRNAs tend to be of poor quality- in my opinion. The major issue I have is that most publications appear- I have not quantified or counted them in any way- appear to follow the one microRNA-one target gene-one publication rule. This "rule" implicates that in the microRNA has one major target, at least in the cell type the publication deals with. Is this really the case? Really?

If you are lucky, you will find a detailed publication on your microRNA of interest and you will get an idea what the major targets of your microRNA are. For most microRNAs this has not been worked out and therefore most databases compiling microRNA targets will be misleading.

You might be much better off by doing your own detailed and comprehensive target gene analysis, functional studies, and eventually a model that tells you which pathways are regulated by this microRNA. This path can be very frustrating and "dangerous". 

You can also take a short-cut and let you guide by gut feeling and intuition and luck: based on how you came up with the microRNAs of interest, what is known about them, how highly they are expressed, what might be good candidate target genes from the literature...

You will not the answer you were looking for in my comment but I am sure within the next days you will receive several answers that will direct you towards the databases of your interest. And you will find lots of data in there. Just be aware that not all what shines beautifully is gold. Bit and bytes in the world wide web are cheap and patiently waiting to be accessed by users. But in the end it is up to you to build a plan on how to make sense of your observations (microRNAs of interest) and put them into a useful model with target genes and pathways.

I hope this helped a t least a little bit.

Hi Maryam... 

I am one of the guys that is going to give you some databases for analyze pathways. Please, pay attention to the observations already pointed out by Thomas. A miRNA is nothing without its cognate targets... You must be aware of these problems.

Here you have some sites to play around

https://sites.google.com/site/mirnatools2/pathway-analysis

By the way, Thomas... you are very pessimistic today. What happens to you?... :)... I am just joking... like always great comments from Thomas. My big respect.

Hope it helps. Best

Paco

Hi Paco,

I once saw these weird Swiss movie that needed subtitles because they spoke Schwitzer Deutsch, a strong German accent, and one line did stick to my brain: pessimism is optimism on the long run. No idea what that is supposed to mean or perhaps I misunderstood since I am not very familiar with Schwitzer Deutsch. I googled it and it seems to be originally a quote from Georg Kreisler.

I am just confused with the dogma that microRNAs have several/many target genes, these target genes are supposed to be pretty consistent between cell types, and all the papers that follow the one microRNA-one target-one publication doctrine. What is your opinion? I am sure there are situations when one microRNA has one major target in the sense that this is the one that can produce a phenotype once affected by the microRNA... But is this the rule or the exception? According to the literature, it is the rule.

Ok Thomas... we can discuss that next time with a good whisky in front...

I agree with you that miRNAs have "major" shots, but the main problem is that eukaryotic cells have millions of compensatory mechanisms to fight against regulators like miRNAs. In my experience some miRNAs are more prone to regulate multiple targets, and this is the richness of the system... Don't you think..

Cheers. Paco

Hi

Thanks for your help and your great comments.

Best

Maryam

The pathways regulated by a miRNA is much dependent on the type of the cell you deal with; I mean a miRNA can regulate different pathways in different tissues. Just ignore these database kind of things... I have a simple (but not easy and cheap) solution: inhibit your miRNA (using antagomir for example), and compare the transcriptome of the treated cells with control cells (like doing RNA-seq); based on this you can find the regulated pathways. And never use miRNA overexpression instead of inhibition for this experiment.

Dear Amir Mizbani

Thanks for your comment.

Could you explain more Why you said"never use miRNA over expression instead of inhibition for this experiment."

Best, Maryam

Hi, the reason is that the real targets of a microRNA are those which are repressed at its normal levels, not when it is overexpressed; overexpression leads to repression of many other genes which are not actual targets. If you compare the list of genes upregulated after inhibition of a microRNA and the list of the genes downregulated after overexpression of that microRNA, they poorly overlap (while you may expect them to be very similar).

One of the newer attempts at bringing a lot of data together is bio4j.  Abstract at http://iwbbio.ugr.es/papers/iwbbio_051.pdf and database at bio4j.com  This may not be sufficiently focused on microRNA for you, but it might be worth a look.  (I am a computer scientist, not a genomics expert.)

Dear Amir and Margaret

Thanks for your help.

Best

Maryam