Question: how to know the gene name for a miRNA and mRNA ? Where is the database ?
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gravatar for aaponcseku
4.2 years ago by
aaponcseku0
Bangladesh
aaponcseku0 wrote:

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 ...

ADD COMMENTlink modified 4.2 years ago by Devon Ryan94k • written 4.2 years ago by aaponcseku0
0
gravatar for Devon Ryan
4.2 years ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

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).

ADD COMMENTlink modified 10 weeks ago by RamRS25k • written 4.2 years ago by Devon Ryan94k
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