Information+about+transcript+expression+levels+4-27-12

Message to Phil 5/3/11

I found the expression levels for all of the genes in my cell line (4T1 breast cancer model cell line for mice). Here they are:

http://www.wip.ncbi.nlm.nih.gov/projects/ geo /query/acc.cgi?view=data&acc=GSM472510&id=9824&db=GeoDb_blob39

The transcript expression information was obtained from the Affymetrix Platform GPL6193 data with a title of "[MoEx-1_0-st] Affymetrix Mouse Exon 1.0 ST Array [probe set (exon) version]" stored on the Gene Expression Omnibus website.

see expression level spreadsheet here "C:\kurt\storage\CIM Research Folder\DR\2013\2-15-13\4T1 transcript expression\4T1 expression info 2-15-13.xlsx"

The format of data in that link is just like this:

EASANA (GenoSplice technology) ID_REF VALUE 4304927 3.503626 4304928 11.62965 4304938 8.141499 4304943 6.985802 4304949 9.352117 4304956 5.859744 4304969 13.40372 4304972 6.774592 4304978 10.1905 4304981 8.179177 . . ..
 * 1) ID_REF =
 * 2) VALUE = Quantile normalized exon level expression values (log2) from

A page describing this data is here:

http://www.wip.ncbi.nlm.nih.gov/projects/ geo /query/acc.cgi?acc=GSM472510

However, I'm not sure what this data means. I don't know which genes each "ref_id" refers to, and I don't know how the value was determined. I know the value is the relative expression level of each mRNA, but I don't know what it was compared to. Is this standard knowledge, or do I need to read their paper or do more searching to find the answers to these questions?

Phil's reply

http://www.wip.ncbi.nlm.nih.gov/projects/ geo /query/acc.cgi?acc=GPL6193

This is the page that describes the platform, the GPL6193 which is an exon array from Affymetrix. Look at the bottom of the page and you'll see the conversion table that goes from probename (ID_REF) to whatever (chromosomal location, gene name, refseq, etc.).

Hope that helps;

Phil