Question: Using BioMart in Ensembl to convert Affy-id to ENSG-genes
0
gravatar for Anna
2.7 years ago by
Anna0
Anna0 wrote:

Hi! I am a beginner in Bioinformatics and have a BioMart question. I have microarray Affy-id:s from Affymetrix Mouse Genome 430 2.0 Array and want the corresponding ENSG-ids from BioMart. The Array has 45 101 Affy-id:s, but I only get 33 750 corresponding ENSG-id:s in BioMart. Can I expect a 1:1 correspondence, or have I used BioMart in the wrong way? As I have understand it reading articles and other questions in the forum about the subject, there may be fewer corresponding ENSG-id:s to the probes?

Also, the microarray experiment I´m analysing is from GEO and was done (submitted) 2007. In this, I already have the corresponding gene names for each probe at the time. Can the probe id corresponding to certain gene(s) have changed or can I trust that the gene - names are the same for the probes today?

//Anna

rna-seq biomart ensembl gene • 1.2k views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Anna0
2
gravatar for Emily_Ensembl
2.7 years ago by
Emily_Ensembl20k
EMBL-EBI
Emily_Ensembl20k wrote:

There is not a 1:1 correspondence between probes and genes for most arrays. There will be some genes missed, there will be some (large) genes with more than one probe.

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Emily_Ensembl20k
0
gravatar for Anna
2.7 years ago by
Anna0
Anna0 wrote:

Thank you Emily!

Just one more question..What I actually ment was that the number of uniq probes was 33 750 and fewer than the 45 101 uniq probes from Mouse Genome 430 2.0 Array that I got from GEO. This array should contain more probes, but maybe it has something to do about your mapping of the probes?

//Anna

ADD COMMENTlink written 2.7 years ago by Anna0
1

BioMart will only return probes that map to genes. If they map to non-genic regions then you won't get them back in BioMart. This is because BioMart is examining the gene database.

ADD REPLYlink written 2.7 years ago by Emily_Ensembl20k
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