Hi Zean,

as far as I know,  miRTarBase is manually curated database of miRNA targets. here you can find whether the miRNA you are looking for, is already being found in the pathway you are interested in by others or not. I my opinion. as the this is experimentally validated targets and taken from literature so you can rely on this .

Quoting form DIANA webpage:

"The arsenal of DIANA Tools ranges from target prediction algorithms (microT v4 and microT-CDS), databases of experimentally verified miRNA targets on coding and non-coding RNAs (TarBase and LncBase) to software capable of identifying potentially altered molecular pathways by the expression of a single or multiple miRNAs (mirPath)."

so if you are using DIANA target prediction then it might differ a little bit. but database results should be consistent with that of the miRTarBase.

The another one you mentioned describes about microarray only so this should be a subset of that you would have found in miRTarBase, only if it concerns with validated results (I was not aware of this site earlier, so can not say much.)

Hi Debasish, thanks a lot! I hope I could touch you if there is any more questions. 

Yes, these databases are shiny, nice, well-maintained and provide a lot of false positive target genes. I would not even put too much trust in databases using "validated" target genes. This is a messy issue and although this is a scientific issue, it is still driven by relatively huge amounts of gut feeling. If you want to know whether your microRNA of interest is involved in the regulation of a specific pathway, you already rely on other "databases" that define this pathway. So all is based on pretty shaky compilations of data, predictions of targets, validated target genes based on the individual preferences of scientists, and very few global, in depth analyses of real and comprehensive target genes.

My advice: you have to generate such data yourself or become a victim of the fallacy of database mania. Don't get me wrong: there is a lot of very good data but there are all a lot of microRNAs. The chances that you find a comprehensive dataset for your microRNAs is slim. Start manipulating your microRNA of interest and you will find the answers you are looking for. 

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Thanks Thomas, I can't agree with more. The fact is that I get more than thirty miRNA from a microarray result and I want to find out which one is involved in the pathway I interested. Do you have any suggestion on the analyses about microarray data? 

Dear Zhen,

you may try the DAVID database. I got nice results using this database. DAVID means "Database for Annotation, Visualization and Integrated Discovery" (http://david.abcc.ncifcrf.gov/home.jsp). There is a Nature-paper describing the usage. Please note that you need the predicted (or confirmed) gene targets of the microRNAs bevore you can do a pathway analysis.

Oliver

Dear Zhen,

if you have 30 candidate miRNAs then it is probably useful to make some tough decisions about their relevance for your cell type or comparison of states. Let's assume you found 30 microRNAs differentially expressed. First thing I would do is eliminate from this pool all the microRNAs that are not well expressed but for some reason up-regulated but still not highly expressed. They may be important but are unlikely candidates. Once you eliminated these "minor" players, you might want to select those with the most dramatic changes, almost black and white. Such extremes rarely exist and you have to rely a little bit on guesswork to come up with a few top relevant candidates. Since you will have focused on the ones with robust and strong expression, there will be most likely a lot of data in the databases about their target genes. 

I have to admit that it is difficult to narrow down the number of microRNAs that should be studied and determine their importance for the observed phenotype. SOmetimes common sense can be a good guide, sometimes common sense will lead you down the path of least resistance and produce common sense data that are already out there. 

I like Targetscan for several reasons. Targetscan is very dogmatic and can be a good starting point. Check out the major hubs of your pathway of interest and how they are predicted to be targeted by your candidate microRNAs. Check if someone has tested a microRNA-target gene interaction for your pair.

Otherwise I suggest you have to start from scratch. I am not sure why you are "obsessed" with a specific pathway (because you manipulated this pathway and saw changes in the 30 microRNAs????), but you may want to approach the issue as unbiased as possible.