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README.Rmd
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README.Rmd
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---
title: '*SIRT4* comutations in CRC'
author: "Joshua Cook"
date: "6/15/2020"
output:
github_document:
html_document:
theme: paper
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, comment = "#>", dpi = 300, cache = TRUE)
```
## Directive from Prof. Kevin Haigis
> A very important collaborator is trying to finish up a grant on SIRT4 in colon cancer.
> SIRT4 mutation is rare, but I noticed from a quick check of cBioportal that when SIRT4 is mutant, KRAS mutations are infrequent (20%), PIK3CA mutations are frequent (almost 50%), and BRAF mutations are frequent (26%).
>
> 1. Could you please do a more rigorous analysis of this in your larger dataset? I believe that PI3K pathway mutations are even more frequent than just looking at PIK3CA. Could you include PTEN and PIK3CG in a separate analysis?
> 2. We would like to include SIRT4 deletion in addition to mutation, since this is a more frequent event. Is that possible?
> 3. Also, my suspicion is that BRAF is enriched because it co-mutated with PIK3CA. Would you agree?
## Analyses
Follow the steps listed below to re-run the analysis on O2:
1. Run `Rscript src/get-data-from-comutation-project.R` to get the data from the *KRAS* comutation analysis.
2. Run `Rscript -e rmarkdown::render('src/sirt4-comutation-analysis.Rmd')`
## Conclusions
[Analysis Markdown](./src/sirt4-comutation-analysis.md)
There were patterns of comutation between *SIRT4* and the key members of the PI3K signaling pathway, particularly with *PIK3CA* and *PIK3CG*.
These genes were also identified as strong predictors of a *SIRT4* mutation in a binomial model.
