I have some problem understanding the data from cBioPortal.
For example, refer to the cell line HCC1428.
For this cell line TP53 is reported as DeepDeleted, but its mRNA z-score is 0.79 (then, it is overexpressed).
Isn't this contradictory?
What am I missing? Could you help me understand this piece of information?
1 answer
Just in case Cyriac does not pick it up:
a Z-score of 0.79 is virtually meaningless, statistically speaking. It indicates that it's expression level is just 0.79 standard deviations above the mean, which is going to be very far from being statistically significant.
We may not be seeing any signal at all for TP53 because it is the gene that is most overly expressed across all carcinomae; thus, despite being 'deep deleted', it is undoubtedly still present in some low-level tumour clones that were sequenced in the TCGA, and, in these clones, it may very well have been over-expressed.
Just a logical explanation
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Tagging: Cyriac Kandoth
Off topic: Nice user name!