Tuesday, April 14, 2015

MicroRNA database : Mirbase naming convension ; Target Database


MirTarBase V 4.5


For human, It has  targets for 596 mature microRNA from mirBase.

Mirbase 20

Number of precursor micorRNA:  1871 ID , 1870 Name (mir-511 has two id)
Number of mature micorRNA:   2794 ID , 2576 Name.

ID 


Each precursor and mature microRNA has unique ID. If you work on ID that would be fine.

 Name  -- > ID

Precursor microRNA
For each primary ID  there is 1 primary name, except one case hsa-mir-511. This name is common for two primary transcript

chr10    .    miRNA_primary_transcript    17887107    17887193    .    +    .    ID=MI0003127;Alias=MI0003127;Name=hsa-mir-511

chr10    .    miRNA_primary_transcript    18134036    18134122    .    +    .    ID=MI0003127_2;Alias=MI0003127;Name=hsa-mir-511

mature microRNA
For each mature name there can be N mature RNA ID .


Target of matureRNA -> target of Precursor microRNA


Option 1
1. map matrueRNA name  : to matureRNA Name set (here you need to check mir-511 manually)


Option 2
1. map matrueRNA name  : to matureRNA ID set
2. map mature RNA ID set  : to precursor RNA ID set
3. include the targets for all member of primary RNA ID set .





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