Introduction to CBioPortal

Augustin Luna
26 January, 2016

Research Fellow
Department of Biostatistics and Computational Biology
Dana-Farber Cancer Institute

Topics to be Covered

  • CBioPortal overview
  • Data retrieval from CBioPortal using cgdsr
    • List cancer datasets
    • List data types for dataset
    • List case sets
    • Retrieve data for selected genes
    • Retrieve clinical data
  • Plotting retrieved data

What is CBioPortal?

Accessing CBioPortal

CBioPortal Data Types

  • NOTE: Not all samples will have complete data
    • DNA copy number variation
    • mRNA expression
    • microRNA expression
    • Mutation profiles
    • Protein and phosopho-protein expression
    • DNA methylation
    • Limited de-identified clinical data

CBioPortal Data Notes

  • Notes on the available data
  • Example notes
    • Clinical data, includes: overall and disease-free survival, gender, age, stage and tumor grade, when available.
    • mRNA and microRNA data is z-scored (i.e. the number of standard deviations away from the mean of expression

CBioPortal Website Features