Question: The gene TGFb isn't measured in Affymetrix HT Human Genome U133 Array Plate Set?
0
gravatar for fernandov
3.8 years ago by
fernandov10
fernandov10 wrote:

Hello, I'm just starting in bioinformatics and bioconductor. It happens that I recently downloaded a microarray of gene expression (Affymetrix HT Human Genome U133 Array Plate Set) from TCGA (data level 3) glioblastoma and I'm interested in the expression of TGFb, but I couldn't find it in any of the rownames of the measures (which I think that are the codes of the genes). That means that the TGFb isn't mesured in this microarray platform?

microarrays tcga gene • 1.1k views
ADD COMMENTlink modified 3.8 years ago by DVA530 • written 3.8 years ago by fernandov10

Can't you find it under any of its aliases?

ADD REPLYlink written 3.8 years ago by Benn7.9k

by aliases you mean TGFB1, TGFB2,... and things like that? If it is, then no, I can't find a gen with the string "TGFB" in its name.

ADD REPLYlink written 3.8 years ago by fernandov10

Can you show the first 6 of your rownames? Maybe there are not gene symbols?

ADD REPLYlink written 3.8 years ago by Benn7.9k

The first 6 are: AACS, FSTL1, ELMO2, CREB3L1, RPS11, PNMA1

ADD REPLYlink written 3.8 years ago by fernandov10

Hello @CharlesWarden and @Helene. Thanks for your help. After reading your answers about that there is TGFB1, I checked again and all of these are in the microarray: TGFB3 TGFBR2 TGFBR3 TGFB1I1 TGFBI TGFBRAP1 TGFB2 TGFBR1 TGFB1 it seems I was doing something wrong and I stayed confused. I apologize for that, and thanks for your answers.

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by fernandov10
2
gravatar for Charles Warden
3.8 years ago by
Charles Warden7.6k
Duarte, CA
Charles Warden7.6k wrote:

You can always look up genes in NetAffx:

https://www.affymetrix.com/analysis/index.affx

Also, I don't see your issue with the TCGA level-3 data (which provides one expression level per gene). For example, there is a value for TGFB1 in this file.

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Charles Warden7.6k
1
gravatar for DVA
3.8 years ago by
DVA530
United States
DVA530 wrote:

These arrays usually cover wide range of genes. I briefly checked the company's annotation list (link, scroll down), and could find TGFB1 in column name "Gene Symbol" row 1060.

Do you know when was your data collected? because old array sometimes does have much narrower gene lists.

ADD COMMENTlink written 3.8 years ago by DVA530
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