Using BioMart in Ensembl to convert Affy-id to ENSG-genes

Question

[Anna]

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

Answer 1

[Emily]

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.

Answer 2

[Anna]

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

[Emily]

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.