Information about transcript expression levels 4-27-12

2015-01-13

azim58 - Information about transcript expression levels 4-27-12

Message to Phil 5/3/11

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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&amp;ac
c=GSM472510&amp;id=9824&amp;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:

#ID_REF =
#VALUE = Quantile normalized exon level expression values (log2) from
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
. . . .

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?

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Phil's reply

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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

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