TPMs for some mitochondrial genes in TCGA are inconsistent with the original TCGA RNA-seq level

[An Zheng]

Hi,

Recently I found something weird to me. TPMs for some mitochondrial genes such as MT-TP, MT-TM and MT-TC are zero for 99% of TCGA cancer samples in your toil RNA-Seq recomputing result. However, these genes are average-expressed (TPM) hundreds to thousands in TCGA data. Could you explain why this happened? Thank you.

Zheng An

[Mary Goldman]

Hi Zheng,

I see what you're saying for the MT-TP gene you mention between the latest batch-effects-normalized expression data from the PanCan Atlas and the data from the Toil pipeline: https://xenabrowser.net/heatmap/?bookmark=eec42d959744500cae81943644362c74. 

I am ccing the author of the Toil dataset so that they can comment.

Best,

Mary

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Mary Goldman, Design and Outreach Engineer

UCSC Xena

UC Santa Cruz Genomics Institute

Revealing life's code

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