Difference between revisions of "Module 4: How does feature selection impact integrative clustering analysis?"
Line 1: | Line 1: | ||
− | * Title: "How | + | * Title: "How do "our expectations" confound the results of our analyses?" |
− | * Paper to be examined: | + | * 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 | + | * 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 | * Data and Code | ||
* Schedule: | * Schedule: | ||
− | ** H1: General introduction to the paper | + | ** H1: General introduction to the cancer genomics concepts and motivation introduced in the paper |
− | ** H2: | + | ** H2: The concept of random expectation (the null model) |
− | ** H3: | + | ** H3: How should we model cancer heterogeneity to estimate the significance of mutual exclusivity? |
− | ** H4-5: | + | ** H4-5: Use R to load and analyze the first cancer genomics dataset (compare alteration distributions and permutation models) |
− | ** H6: | + | ** H6: Reproduce mutual exclusivity analyses proposed in the original paper. |
− | ** H7-8: | + | ** H7-8: Examine TCGA cancer genomic studies to perform mutual exclusivity analyses under different permutation models |
− | ** H9: Summarize results | + | ** H9: Summarize and present the results. |
* Key bioinformatics concept of this module: | * 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"]] | * back to [[UNIL MSc course: "Case studies in bioinformatics 2015"]] |
Latest revision as of 19:44, 23 November 2015
- 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