How To Standardize Probe Ids With Ailun?

Question

[Layla]

Hi: I have got some signatures obtained from SAM and performed on GEO datasets, like for example GDS 1528. The data from SAM has the following format

Row             Gene ID          Gene Name            Score(d)
19394             1451330_a_at        19393             46.83481995

In one paper I read the following:

we standardize gene identifiers from chip-specific probe identifiers to NCBI GeneID identifiers usin g AILUN

In the part when the author mentions PROBE IDENTIFIERS, that she/he refers to the value of GENE_ID? so that it makes it match with a standard gene name in ENTREZ? How I can do that standardization using AILUN? Thanks for your help

Answer 1

[Istvan Albert]

You should link the paper in your question so that people understand the context a little better.

AILUN is a web service offered via http://ailun.stanford.edu/

Among other services it is able to map a probe id to a NCBI gene identifier, see the Platform Annotations link. For your example 1451330_a_at it generates:

No. GPL ID Title Species % of Matched Probe ID
1339[MOE430A] Affymetrix Mouse Expression 430A ArrayMus musculus100.00
27440NuGO array (mouse) NuGO_Mm1a520177Mus musculus100.00
38321[Mouse430A_2] Affymetrix Mouse Genome 430A 2.0 ArrayMus musculus100.00
48759[HT_MG-430A] Affymetrix HT Mouse Genome 430A ArrayMus musculus100.00
51261[Mouse430_2] Affymetrix Mouse Genome 430 2.0 ArrayMus musculus100.00

(that being said the links there do not seem to not work properly - it could be some setting problem, ask the people that run the service)

Also it seems one can call some of these services directly from R.

[Layla]

thanks for your help, the name of the paper is: Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data