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Module 3

In this module you will apply what was learnt in the Bioconductor module (module 2) to a challenging microarray experiment from a recent Nature paper. You will analyze the activation status of several human oncogenic pathways. You will validate the signatures found in tumor samples derived from various mouse cancer models. Association with disease outcome of the oncogenic pathway signatures will be validated for various publicly available human cancer datasets.

Course material


  • Oncogenic pathway signatures in human cancers as a guide to targeted therapies pdf html suppl more suppl GEO data. Andrea H. Bild et al, Nature 439, 353-357 (2006)
  • Cancer biology: Signatures guide drug choice pdf html. Julian Downward, Nature 439, 274-275 (2006)
  • More information about the classification methods used in Bild et al can be found in: Predicting the clinical status of human breast cancer by using gene expression profiles pdf html, Mike West et al, PNAS 98, 11462-11467 (2001)
  • GEOquery package: vignette



A report (pdf/word) explaining your approach and results together with R code has to be handed in (Perry Moerland) before May 27th (23:59 pm), 2011. Your report should follow this format:

  • Repeat the question
  • Short motivation of your R code and the R code itself, comments in the code are appreciated
  • Results, figures, and small tables in the text. Large tables should go to an appendix.
  • Discussion of the results and/or answer to the question
  • Also put all your R code in one separate .R file so that the code can be easily checked.

Good luck!
Topic revision: r2 - 04 Apr 2011, PerryMoerland Search
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