TCGA survival by gene expression. Gene is missing everywhere I look, but should be possible?

Question

[hgalmoore]

Hello,

I am trying to generate TCGA survival plots with gene expression data. I found a few interesting guides out there, but the genes I am interested in don't work. The genes I want to look at are TRDC, TRDV1, TRDV2 in COAD and UCEC. When I download the data from GDAC (http://gdac.broadinstitute.org/) or from a R package like RTCGA.mRNA, the three genes above are missing from the normalized counts as well as the raw count files for these samples. My understanding is that it should be possible to see these genes in TCGA data somehow because one of my collaborators (who is a statistician) was able to generate survival plots for these genes expression levels.

Can someone tell me what I am doing wrong? I thought it was that these lower expression genes were filtered out, but they should've still been present in raw counts, no?

Thanks.

Answer 1

[Zhenyu Zhang]

most likely a gene name mapping problem you can try to

• obtain gdac gene model (I think it's a gaf file) and look at the coordinate to see if your gene has a different name
• go to ensembl to map your genes to possible ensembl gene ids, and then go to GDC for expression data