Introduction to CBioPortal Augustin Luna 20 January, 2016 - PowerPoint PPT Presentation

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Introduction to CBioPortal Augustin Luna 20 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

Introduction to CBioPortal Augustin Luna 20 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? Publication: http://www.ncbi.nlm.nih.gov/pubmed/23550210 Provides molecular profiles and clinical attributes from large-scale cancer genomics projects Dataset List http://www.cbioportal.org/data_sets.jsp Datasets Total 105 datasets (as of Jan. 2015) TCGA: The Cancer Genome Atlas Cancer Cell Line Encyclopedia NCI-60 (no drug response data) Other collected large-scale datasets from publications
Accessing CBioPortal Interactive Website: http://www.cbioportal.org/ Project provides an application programming interface (API) Makes CBioPortal accessible from any programming language http://www.cbioportal.org/web_api.jsp cgdsr R Package simplifies access to the CBioPortal API
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 http://www.cbioportal.org/faq.jsp 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
CBioPortal Tutorials
CBioPortal Datasets
CBioPortal Home Data Selection
CBioPortal OncoPrint
CBioPortal Plots
CBioPortal Mutations
CBioPortal Survival
CBioPortal OncoPrinter
CBioPortal Mutation Mapper
CBioPortal Study: Summary
CBioPortal Study: Clinical Data
CBioPortal Patient: Summary
CBioPortal Patient: Drug Targets
CBioPortal Patient: Histology
CBioPortal Patient: Pathology
CBioPortal Patient: Copy Number
CBioPortal Patient: Network
What is cgdsr? Website and Tutorial (Vignette): https://cran.r-project.org/web/packages/cgdsr/index.html Provides programmatic access to CBioPortal data
Getting Help CBioPortal Google Group http://groups.google.com/group/cbioportal Biostars https://www.biostars.org/t/cbioportal/

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