Noob question: I want to use TCGA data to compare survival with mutations, how should I do it?

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2.5 years ago

cdeantoneo31 ▴ 20

First I am a huge noob to bioinformatics and most of my knowledge is self taught, so please excuse my lack of vocabulary and just overall dumbness

My PI would like us to compare survival of cancer patients who have knock out/loss of function mutations in gene a, ko/lof in gene b, and fully functional gene A with ko/lof gene b.

My question is: what is the best way to do this? Should I use R and the TCGA R tools, or is there a more user friendly tool?

cancer mutations tcga • 999 views

ADD COMMENT • link updated 20 months ago by Ram 44k • written 2.5 years ago by cdeantoneo31 ▴ 20

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I have not done this myself, so please take with a grain of salt. I looked around right quick. The "TRGAted" platform appears to perform survival analysis on TCGA data. Check out this article and let me know what you think. Does it help at all? If not, why not and we can go from there

ADD REPLY • link 2.5 years ago by LauferVA 4.5k

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more generally, definitely read the linked wikipedia page on survival analysis. not sure if you have a math or stats background. if not, parsing the notation is non-trivial at first. but irrespective, even if you only understand a fraction of it, will be worthwhile

ADD REPLY • link 2.5 years ago by LauferVA 4.5k

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Will do, tysm!

ADD REPLY • link 2.5 years ago by cdeantoneo31 ▴ 20

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This actually is super helpful, thank you!

My B.S. is in biochemistry, so not super heavy math or stats, but the wikipedia page is definitely understandable

ADD REPLY • link 2.5 years ago by cdeantoneo31 ▴ 20

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