Missing Genes in Datasets

[Samuel Hawkins]

Good afternoon,

 

I am a PhD student based in cardiff university studying prostate cancer. I have been compiling together a figure using some of the prostate cancer datasets available on your website.

 

Whilst I have been successful in creating some very nice figures for PREX2, I have tried using the exact same datasets to produce the same figures for PREX1 with limited success. Is it common for these datasets to have missed out genes in their sequencing and is this an issue from the original dataset itself or am I utilising your website wrong to find this data. I have supplied below the datasets and whether they provide results for PREX2 and/or PREX1.

 

SU2C/PCF Dream Team, Cell 2019 – Both PREX2 and PREX1

MSK/DFCI, Nature Genetics 2018 - Both PREX2 and PREX1

MSK, Clin Cancer Res. 2022 - Only PREX2

MSK, Eur Urol 2020 – Only PREX2

Race Differences in Prostate Cancer (MSK, 2021) - Only PREX2

MSK, Clin Cancer Res. 2020 – Only PREX2   Many thanks, Sam

 

[JJ Gao]

Hi Sam,

PREX1 is not part of the MSK-IMPACT gene panel - one way to check this is to look at the oncoprint and see if the samples are profiled (https://bit.ly/4741QZz).

Best,

-JJ

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