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

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

Dec 25, 2022 241 likes •507 views

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

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Introduction to CBioPortal

Augustin Luna 20 January, 2016 Research Fellow Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute

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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

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What is CBioPortal?

Publication: Provides molecular profiles and clinical attributes from large-scale cancer genomics projects Dataset List 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 http://www.ncbi.nlm.nih.gov/pubmed/23550210 http://www.cbioportal.org/data_sets.jsp

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Accessing CBioPortal

Interactive Website: Project provides an application programming interface (API) Makes CBioPortal accessible from any programming language cgdsr R Package simplifies access to the CBioPortal API http://www.cbioportal.org/ http://www.cbioportal.org/web_api.jsp

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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

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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 http://www.cbioportal.org/faq.jsp

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CBioPortal Website Features

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CBioPortal Tutorials

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CBioPortal Datasets

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CBioPortal Home Data Selection

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CBioPortal OncoPrint

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CBioPortal Plots

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CBioPortal Mutations

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CBioPortal Survival

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CBioPortal OncoPrinter

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CBioPortal Mutation Mapper

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CBioPortal Study: Summary

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CBioPortal Study: Clinical Data

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CBioPortal Patient: Summary

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CBioPortal Patient: Drug Targets

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CBioPortal Patient: Histology

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CBioPortal Patient: Pathology

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CBioPortal Patient: Copy Number

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CBioPortal Patient: Network

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What is cgdsr?

Website and Tutorial (Vignette): Provides programmatic access to CBioPortal data https://cran.r-project.org/web/packages/cgdsr/index.html

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Getting Help

CBioPortal Google Group Biostars http://groups.google.com/group/cbioportal https://www.biostars.org/t/cbioportal/