View source for Module 4: How do "our expectations" confound the results of our analyses?

*  Title: "How do "our expectations" confound the results of our analyses?"

* Paper to be examined: “Mutual Exclusivity analysis identifies oncogenic network modules”, Genome Research 2012 22, 398-406 [http://genome.cshlp.org/content/early/2011/10/12/gr.125567.111.full.pdf]
+ cancer genomic studies from The Cancer Genome Atlas (TCGA). 

* Key claim of the paper: "We introduce here a simple but effective method to evaluate the statistical significance of correlations between genomic events, that concurrently preserves both '''tumor selectivity''' and '''tumor heterogeneity'''" 

* Data and Code
  
* Schedule: 
** H1: General introduction to the cancer genomics concepts and motivation introduced in the paper
** H2: The concept of random expectation (the null model)
** H3: How should we model cancer heterogeneity to estimate the significance of mutual exclusivity?
** H4-5: Use R to load and analyze the first cancer genomics dataset (compare alteration distributions and permutation models)
** H6: Reproduce mutual exclusivity analyses proposed in the original paper.
** H7-8: Examine TCGA cancer genomic studies to perform mutual exclusivity analyses under different permutation models
** H9: Summarize and present the results.

* Key bioinformatics concept of this module: 
** The importance of the null model (your expectations)
** Properly assessed Mutual Exclusivity inform on biological pathways altered in cancer

* back to [[UNIL MSc course: "Case studies in bioinformatics 2015"]]

* Slides
** Slides of the lesson of Monday Dec. 5th: [[Media:module4_slides_2016.pdf]]

* Data and Code
** Data and R code for practical exercise [[Media:exercise.zip]]