I have a list of miRNA IDs and a list of mRNA IDs and they are from Mus musculus species. I have converted the list of mRNA IDs to gene symbols by a list of data that was exist in NCBI and miRNA IDs list to gene symbols using Diana but I got in trouble because gene symbols on NCBI didn't match with the gene symbols that exist in Diana site. I think the problem is that naming of gene symbols doesn't follow a specific rule in different databases and are not standardized. Can anyone tell me a good way to transform both mRNA & miRNA lists to a platform for example unigene that would be unique in all kinds of databases?
For mouse gene names and other details you should refer to the mouse genome informatics database (it is a standard organism-specific database like flybase [Drosophila], SGD [yeast], etc).
However, it is much better to work with RefSeq IDs. Moreover, miRNAs are seldom referred to, using their gene names. Always stick to the miRNA naming convention that is described in miRbase.
I am not sure what you are actually interested in. If you intend to map miRNAs to their targets then you can use one of the standard gene names along with the RefSeq ID. If you are using miRanda or TargetScan to predict the targets then these programs return different identifiers for the target gene including its official gene name.
In general, for ID conversion, I would prefer BioMart.