This is a test version of Biostars. For the public version, visit https://www.biostars.org.
how to know the gene name for a miRNA and mRNA ? Where is the database ?

I am working on computational method to find out target mRNA for some selected miRNA. In NCBI I found expression matrix to do my job. Finally using MiRTarBase to validate my computational result.

In MiRTarBase there is miRNA like, hsa-miR-200a and its target gene like VIM, CHD9 etc.

But, in the expression data from NCBI, the miRNA are represented by an ID like, 3980, 9938 etc.

The mRNA from NCBI are represented by ID like, AFFX-BioB-M_at, AFFX-BioB-M-3_at, etc.

I can see that the ID reference from the two sources for miRNA and mRNA are different. How can I match an ID from NCBI to an ID with MiRTarBase / TarBase? If I have any misconception please clarify

gene mirtarbase mirna-mrna ncbi tarbase
• 2,622 views • link
updated by Ram Ram • written by aaponcseku • aaponcseku

1 answer

But, in the expression data from NCBI, the miRNA are represented by an ID like, 3980, 9938 etc.

For what it's worth, the Entrez ID for hsa-miR-200a is 406983. You can download the Entrez ID to symbol conversion files from UCSC.

The mRNA from NCBI are represented by ID like, AFFX-BioB-M_at, AFFX-BioB-M-3_at, etc.

Those aren't from NCBI, they're from Affymetrix and they're probe IDs for a microarray (they happen to be control probes and shouldn't be binding genes). Find out the appropriate microarray chip ID and you can then download the appropriate mapping file from GEO (like this one).

• 0 views • link
updated by Ram Ram • written by Devon Ryan Devon Ryan

Log in to answer this question.

More posts like this