Affymetrix Gene Id Format - What Does "At" Stand For?

Question

[Davide Chicco]

I am currently using some genes in Affymetrix format, like: - 200007at - 200011sat - 200012x_at

What do "at", "sat", and "x_at" stand for?

Thanx

Answer 1

[Larry_Parnell]

Here is an answer from the Affymetrix FAQ:

The last three characters identify the probe set strand. Probe sets that are designed to detect the anti-sense strand of the gene of interest are annotated with "_at". Probes in an identical probe set (_s set) all cross-hybridize to the same set of sequences that are used for the design (including any additional pruning sequences if provided). Probes in a mixed probe set (_x set) contain at least one probe that cross-hybridizes with other sequence(s) used for the design.

See tjhe above link for more information, including a nice figure depicting these relationships and definitions.

[Fred]

I didn't see your answer before posting mine :)

[Larry_Parnell]

No worries - same link, same good information. I'll vote yours up as I cannot vote up my own response.

Answer 2

[Fred]

You can have some information here:

http://www.affymetrix.com/support/help/faqs/mouse_430/faq_8.jsp

"_at" is related to the strand of the probeset compared to the gene.

"_x_at", "_s_at" and "_a_at" define how the probes are cross-hybridizing. There is a schema in the previous URL.