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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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TERTp mutations and EXTEND scores #1653

Closed sjspielman closed 1 year ago

sjspielman commented 1 year ago

Closes #1651 This PR adds a short script that explores whether samples with specific TERTp mutations C228T and C250T also have higher EXTEND scores, which is part of our reviewer response. There are 9 samples in our data that have these two mutations, and only 6 of those samples have corresponding stranded RNA libraries that we can use for EXTEND score comparison. A wilcox test for EXTEND scores across groups is P=0.1196, so we have no evidence of increased scores for these samples. The sample size is of course tiny though, so this is a major caveat.

My sense is we can pop the figure I made here along with the test results into the response to reviewers, and call it a day? I'm also curious if we prefer for me to make this a notebook since it's more exploratory?

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sjspielman commented 1 year ago

@jharenza I've added in those scatterplots. We see some trend with TERT (all points are above the line except one which is on the line) but less so with TERC. But, this does not really suggest that these samples have higher expression of either gene. TERTp_mutations_TERC_TERT_expression.pdf

jharenza commented 1 year ago

@jharenza I've added in those scatterplots. We see some trend with TERT (all points are above the line except one which is on the line) but less so with TERC. But, this does not really suggest that these samples have higher expression of either gene. TERTp_mutations_TERC_TERT_expression.pdf

Thanks! OK, I think we can use this and explain there is heterogeneity - we see some have high scores and high TERT expression, some low/low, etc, but numbers are low.

sjspielman commented 1 year ago

do you want to change that TERT/TERC ggplot background and we can call it a day - these can go into supplemental

That sounds good to me! But, I'd prefer do that in a separate PR that focuses just on modifying the FigS5 script to include this information, which means this PR would be more exploration towards that end.