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Missing ATP Synthase Genes in TCGA Dataset

So I've been working with the TCGA-LUAD transcriptomics dataset (https://portal.gdc.cancer.gov/projects/TCGA-LUAD) for a while now and just started looking at ATP-synthase. However, 2 of the subunits appear to be missing in this dataset. The two that are missing are MT-ATP6 (ENSG00000198899) and MT-ATP8 (ENSG00000228253). I've checked a couple other datasets from TCGA and they weren't in those either, so I'm wondering if I'm doing something wrong.

Maybe it's a version thing? Or maybe their expression levels are actually contained in a different gene? I know these two genes overlap with each other, so maybe that's part of the issue?

I've seen publications that look at those specific genes in TCGA data, so I don't think it's a sitewide issue. I'm at a bit of a roadblock due to those missing subunits, so any help would be greatly appreciated!

tcga ensembl synthase luad atp
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written by bucksotj • bucksotj

1 answer

Alright, I figured it out. When extracting the data with the following line...

data <- GDCprepare(query)

I always see the message "From the 60483 genes we couldn't map 3881". And I've always just ignored it assuming those 3881 weren't important. Turns out the enzymes I wanted were in those 3881 that couldn't be mapped, so I just had to change it to this:

data <- GDCprepare(query, summarizedExperiment = F)

And now I have their expression data.

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written by bucksotj • bucksotj

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