COnversion of REF_ID into gene name (or the other way around)

Question

[klabunde]

Dear all,

I'm trying to find published datasets regarding the transcriptomic reaction of mice lungs to Streptococcus pneumoniase infection.

I found datasets on GEO, I however can't make anything out of the annotation:

In one case the IDs look like this: ILMN_2735413 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61459)

in another case like this: 100036520_at (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71623)

Is it somehow possible to transform this into gene symbols? Or are these just internal numbers of the group which performed the study?

Thanks a lot for your help!

Answer 1

[Matthias Zepper]

Each GSE entry has a section called Platform, which will provide information on the technology used to generate the data - in your case, two different microarrays. For GSE61459 it is the Illumina MouseWG-6 v2.0 expression beadchip and for GSE71623 Affymetrix Mouse Gene 1.0 ST Array.

Conversion for the two into gene symbols is of course possible, e.g. with BioMart or via the reference tables for the two arrays - see the data tables for MouseWG-6 v2.0 and Mouse Gene 1.0 ST Array. Please mind, that additional normalization is required, if you wish to compare measurements across the respective series.

[klabunde]

Thanks a lot, that was precisely what I needed.