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 [1]

+ 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_051216.pdf

• Data and Code
  • Data and R code for practical exercise