Im working on some analysis with miRNA expression data and miRNA targets information from different sources like miRBase, Targetscan etc... 

The names of miRNAs in the expression data and miRNAs targets information data need to be same for my analysis

But I see that in both of these data, names look different.

For eg: In miRNA expression data, there is a miRNA `hsa-miR-373` and in miRNA target information I see there are `hsa-miR-373-3p, hsa-miR-373-5p`. 

similarly, In expression data `hsa-mir-101-1 and hsa-mir-101-2` and miRNA target information it is `hsa-mir-101-3p`

Question: Can I change the names of `hsa-miR-373-3p, hsa-miR-373-5p` into `hsa-miR-373`? 
miRNA nomenclature can be a bit confusing. The direct answer to your question is yes somtimes, but not always, and not without checking. 

miRNAs are expressed as hairpins. Thus, the precursor hairpin to hsa-miR-373 looks like:

                -     g            uuuuug     |
    5' gggauacuc aaaau ggggcgcuuucc      u    |
       ||||.||.| ||||| |..||.|||.||           | - This is pre-hsa-miR-373
    3' cccuguggg uuuua cuucgugaaggg      c    |
                g     g            ucaugu     |

This is processed to make a double stranded RNA, which contains two short RNAs that could potentially act as miRNAs:

        acuc-aaaaugggggcgcuuucc     <---- This is hsa-miR-373-5p
        ||.| ||||| |..||||||.
      ugugggguuuuagcuucgugaag       <---- This is hsa-miR-373-3p

For most RNAs one of these arms is unstable and is quickly degraded, so it doesn't get chance to have any activity. The other is stable and get incorporated into RISC - the enzyme that does the business for miRNAs.  In the case of hsa-miR-373 the 3p arm is stable and the 5p arm is unstable. Thus the 3p arm is also known as hsa-miR-373 and the 5p arm is also known as hsa-miR-373*. You can't treat hsa-miR-373-5p/miR-373* as the same as miR-373, because it has an entirely  different sequence, and would have different targets if it were ever stable enough to get incorporated in to RISC. The information on which arm is which is in mirbase. There are some miRNAs however, where both arms are stable and must be treated as independent miRNAs. 

The next complication is that some miRNAs appear more than once in the genome. hsa-miR-101 is an example of this. hsa-miR101-1 is located on chromosome 1, and hsa-miR-101-2 is located on chromosome 9. But both encode miRNA precursors that have identical 3p arms. That is the sequence of the 3p mature miRNA product produced from both the hsa-miR-101-1 and hsa-miR-101-2 loci is `uacaguacugugauaacugaa`, and this is the stable arm. If you sequence this, you have no idea whether it came from miR-101-1 or miR-101-2. However, the unstable 5p arms are different for miR-101-1 and miR-101-2. So officially there are 3 mature miR-101 RNAs in humans - miR-101-1-5p, miR-101-2-5p and miR-101-3p, expressed from two loci.  In this case you can safely treat miR-101-3p as miR-101 irrespective of which locus it came from. Sometimes both arms are identical.  Again, the information on which mature products are the same between the two copies, and which is the stable and unstable arm, is on mirbase. 



