cBioPortal
cBioPortal
Introduction
1. General
News
Frequently Asked Questions
About Us
List of RFCs
2.1 Deployment
Architecture overview
Hardware Requirements
2.1.1 Deploy with Docker (Recommended)
Deploy with Docker
Example Commands
Authenticating and Authorizing Users using Keycloak in Docker
2.1.2 Deploy without Docker
Software Requirements
Pre-Build Steps
Building from Source
Importing the Seed Database
Deploying the Web Application
Loading a Sample Study
2.2 Authorization and Authentication
User Authorization
Authenticating Users via SAML
Authenticating Users via LDAP
Authenticating and Authorizing Users via Keycloak
Authenticating Users via Tokens
2.3 Customization
Customizing your cBioPortal Instance via portal.properties
More portal.properties Settings
Configuring Caching Behavior
2.4 Integration with Other Webservices
OncoKB Data Access
3. cBioPortal Maintenance
Updating your cBioPortal Database Scheme
Update genes and gene aliases
4. Development
cBioPortal Entity-relationship Diagram
Using the Data Manager to Get Data and Set Session Parameters
Accessing Services via the Web-API
Providing cBioPortal Parameters
Manual test cases
Build cBioPortal with a different frontend version
Release Procedure
Deployment Procedure
5.1 Data Loading
Data Loading Overview
5.2 Datasets
Downloads
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News

Feb 12, 2020

Feb 6, 2020

  • New Feature: Extend the recent group comparison feature by allowing comparisons inside the Results View page. The new tab allows for quick comparison of altered vs unaltered cases by survival, clinical information, mutation, copy number events and mRNA expression:

    ​​group_results640px​​

  • Performance enhancement: the Study View's mutation table now loads faster for studies with multiple gene panels. For the genie portal, which has a study with many different gene panels this resulted in a speed-up from ~90-120 seconds to 5 seconds.

  • Read more about the v3.2.2 release here​

Jan 30, 2020

  • Enhancement: Show HGVSg in mutations table and linkout to Genome Nexus:

    ​hgvsg genome nexus​

  • Enhancement: Add a pencil button near gene list in results page which opens interface for quickly modifying the oql of the query:

    ​edit query pencil​

  • See more updates here​

Jan 29, 2020

Dec 19, 2019

  • Enhancement: We restored support for submitting large queries from external applications using HTTP POST requests. Accepted parameters are the same as appear in the url of a query submitted from the homepage.

  • See more updates here​

Dec 12, 2019

  • Enhancement: Several enhancements to the display of gene panels on the Patient View page, by The Hyve, described in more detail here​

    ​image​

  • Enhancement: Add Count Bubbles to Oncoprint Toolbar

    ​Screenshot from 2019-12-06 11-36-21​

  • See more updates here​

Nov 29, 2019

  • Enhancement: Support group comparison for custom charts in Study View page

  • Enhancement: Performance improvement of Co-Expression analysis.

  • Enhancement: Kaplan-Meier plots now supports custom time range.

  • See more updates here​

Nov 22, 2019

  • New Feature: Support for Treatment response data in the Oncoprint and Plots tab, including new Waterfall plot type. Read more in The Hyve's blog post​

image

Nov 15, 2019

  • Enhancement: heatmap tracks in OncoPrint now has separate headers and sub-menus. example​

image

  • Enhancement: global settings for query session

Nov 7, 2019

Oct 30, 2019

October 23, 2019

  • Enhancement: Quick example links in Plots tab. example​

October 14, 2019

  • New Feature: Fusion Genes table in Study View. example​

image

October 11, 2019

  • Enhancement: The Download interface on the homepage has been removed. Enhanced download functionality is now available after querying on the results page.

    Home page:

    ​homepage download tab removed​

    Results page:

    ​results page download tab​

    Note that as before one can always download the full raw data on the Data Sets page or from Datahub.

October 9, 2019

September 18, 2019

  • New Feature: The list and order of charts of a study will be automatically saved now as a user preference on the study view page.

September 6, 2019

August 13, 2019

July 26, 2019

June 19, 2019

  • New Feature: Show Genome Aggregation Database (gnomAD) population frequencies in the mutations table - see example:

    ​gnomad feature news​

June 12, 2019

​​group-comparison​​

May 8, 2019

  • New Feature: Show Post Translational Modification (PTM) information from dbPTM on the Mutation Mapper - see example:

    ​ptm feature_news​

April 26, 2019

March 29, 2019

  • New Feature: Use the new quick search tab on the homepage to more easily navigate to a study, gene or patient:

    ​quick_search_news​

March 15, 2019

February 22, 2019

  • Enhancement: Exon number and HGVSc annotations are available in optional columns in the Mutations tab on the Results page and in the Patient View.

  • New feature: option to a show regression line in the scatter plot in the Plots tab on the Results page

image

February 19, 2019

  • New feature: Copy-Number Segments tab on the Study View page using igv.js v2 - see example​

  • Improved Copy-Number Segments tab on the Results page

  • New feature: OncoKB and Cancer Hotspots tracks in the Mutations tab on the Results page

image

January 24, 2019

December 17, 2018

  • The 10th phase of cBioPortal architectural upgrade is now complete: the Study View has been moved to the new architecture with numerous improvements. This marks the completion of the cBioPortal architectural refactoring! 🎉🎉🎉

​​image​​

October 29, 2018

  • The ninth phase of the cBioPortal architectural upgrade is now complete: the results page is now a single-page application with better performance.

  • Supported plotting mutations by type in Plots tab

image

October 19, 2018

mutation_mapper_dropdown

October 17, 2018

image

August 7, 2018

  • The eighth phase of the cBioPortal architectural upgrade is now complete: The Plots, Expression, Network, and Bookmarks tabs, and therefore all analysis tabs in the results page, have been moved to the new architecture.

  • Updated the MutationMapper tool, now connecting to Genome Nexus for annotating mutations on the fly.

  • Total Mutations and Fraction Genome Altered are now available in Plots tab for visualization and analysis.

  • Enhanced clinical attribute selector for OncoPrint, now showing sample counts per attribute.

    ​image​

July 27, 2018

June 20, 2018

  • The seventh phase of the cBioPortal architectural upgrade is now complete: The Enrichments and Co-Expression tabs have been moved to the new architecture.

  • Supported merged gene tracks in OncoPrint and Onco Query Language -- see example​

image

May 10, 2018

  • Enhanced OncoPrint to show germline mutations -- see example​

    ​image​

April 17, 2018

April 05, 2018

March 20, 2018

  • The sixth phase of the cBioPortal architectural upgrade is now complete: The Download tab has been moved to the new architecture.

  • Data can now be downloaded in tabular format from OncoPrint.

  • Added an option to download an SVG file on the Cancer Type Summary tab.

    ​image​

January 15, 2018

  • The fifth phase of the cBioPortal architectural upgrade is now complete: The OncoPrint and Survival tabs have been moved to the new architecture.

November 20, 2017

October 17, 2017

  • The fourth phase of the cBioPortal architectural upgrade is now complete: The Mutual Exclusivity and Cancer Type Summary tabs have been moved to the new architecture.

  • Updated protein structure alignment data in Mutations tab are now retrieved from Genome Nexus via the G2S web service.

October 2, 2017

June 26, 2017

  • The second phase of the cBioPortal architectural upgrade is now complete: The query interface now has a fresh look and faster performance.

    ​image​

May 12, 2017

May 5, 2017

  • First phase of cBioPortal architectural upgrade complete: Patient view now has fresh look and faster performance. example​

March 28, 2017

  • New features:

    • Per-sample mutation spectra are now available in OncoPrints -- see example​

    ​image​

    • mRNA heat map clustering is now supported in OncoPrints

    • MDACC Next-Generation Clustered Heat Maps are now available in the patient view

    • cBioPortal web site style change

Feburary 2, 2017

  • New features:

    • 3D hotspot mutation annotations are now available from 3dhotspots.org

  • New data:

    • CPTAC proteomics data have been integrated for TCGA breast, ovarian, and colorectal provisional studies

December 23, 2016

  • New features:

    • Heat map visualization of gene expression data in the OncoPrint

    ​OncoPrint Heatmap​

    • Heat map visualization of gene expression data in the Study View page connecting to MDACC's TCGA Next-Generation Clustered Heat Map Compendium

October 7, 2016

  • New features:

    • All data sets can now be downloaded as flat files from the new Data Hub​

    • Annotation of putative driver missense mutations in OncoPrints, based on OncoKB, mutation hotspots, and recurrence in cBioPortal and COSMIC

    ​OncoPrint-OncoKB​

    • Copy number segments visualization directly in the browser in a new CN Segments tab via IGV.js​

    ​image​

  • Improvements:

    • Improved cancer study view page (bug fixes and increased performance)

July 24, 2016

June 6, 2016

  • New features:

    • Annotation of mutation effect and drug sensitivity on the Mutations tab and the patient view pages (via OncoKB)

      ​oncokb-screenshot​

  • Improvements:

    • Improved OncoPrint visualization using WebGL: faster, more zooming flexibility, visualization of recurrent variants

    • Improved Network tab with SBGN view for a single interaction

    • Performance improvement of tables in the study view page

    • Mutation type summary on the Mutations tab

March 31, 2016

January 12, 2016

December 23, 2015

  • New features:

    • Visualization of RNA-seq expression levels across TCGA studies (cross-cancer queries)

      ​cross cancer expression​

    • Selection of genes in the study view to initiate queries

      ​query gene in study view​

  • Improvement:

    • 3-D structures in the "Mutations" tab are now rendered by 3Dmol.js (previously JSmol)

    • Improved performance by code optimization and compressing large data by gzip

December 1, 2015

  • New feature: Annotated statistically recurrent hotspots, via new algorithm by Chang et al. 2015</br>

    ![Annotate recurrent hotspots](https://cloud.githubusercontent.com/assets/840895/11794851/7729839e-a281-11e5-9413-12dc885b947d.png)

November 9, 2015

  • New features:

    • Links to MyCancerGenome.org for mutations

      ​Link to MyCancerGenome.org​

    • Improved display of selection samples on the study view page

  • Improvements:

    • "Enrichments" analysis is now run across all genes

    • The "Network" tab is now using Cytoscape.js (Adobe Flash is no longer required)

October 6, 2015

August 21, 2015

  • All TCGA data updated to the Firehose run of April 16, 2015.

  • New feature: Enrichments Analysis finds alterations that are enriched in either altered or unaltered samples.

  • Improvement: improved OncoPrint with better performance.

June 3, 2015

  • Improvements:

    • Allowed downloading data in each chart/table in study summary page.

    • Added log-rank test p-values to the survival plots in study summary page.

    • Improved visualization of patient clinical data in patient-centric view.

    • Added option to merge multiple samples for the same patient in OncoPrint.

April 28, 2015

  • New features:

    • Redesigned query interface to allow selecting multiple cancer studies

    • Redesigned Plots tab

January 20, 2015

  • All TCGA data updated to the Firehose run of October 17, 2014

  • COSMIC data updated to V71

  • New features:

    • Query page: better search functions to find cancer studies

    • OncoPrints now support color coding of different mutation types

    • OncoPrints now support multiple clinical annotation tracks

    • ​OncoPrinter tool now supports mRNA expression changes

      ​Oncoprint with multiple clinical tracks​

January 6, 2015

  • New feature: You can now view frequencies of mutations and copy-number alterations in the study view. These tables are updated dynamically when selecting subsets of samples.

    ​Alterations in heavily copy-number altered endometrial cancer cases​

December 9, 2014

October 24, 2014

August 8, 2014

  • Released two new tools

    • ​Oncoprinter lets you create Oncoprints from your own, custom data

    • ​MutationMapper draws mutation diagrams (lollipop plots) from your custom data

May 21, 2014

  • All TCGA data updated to the Firehose run of April 16, 2014

May 12, 2014

March 27, 2014

  • New features:

    • Visualizing of mutations mapped on 3D structures (individual or multiple mutations, directly in the browser)

    • Gene expression correlation analysis (find all genes with expression correlation to your query genes)

    • The Patient-Centric View now displays mutation frequencies across all cohorts in cBioPortal for each mutation

    • The Mutation Details Tab and the Patient-Centric View now display the copy-number status of each mutation

      ​3D viewer & Co-expression​

March 18, 2014

  • All TCGA data updated to the Firehose run of January 15, 2014

  • Updated to the latest COSMIC data (v68)

  • Added two new provisional TCGA studies:

    • Adrenocortical Carcinoma

    • Uterine Carcinosarcoma

  • Added mutation data of 898 samples from 11 published studies:

    • Hepatocellular Carcinoma (RIKEN, Nature Genetics 2012)

    • Hepatocellular Carcinoma (AMC, Hepatology in press)

    • Medulloblastoma (Broad, Nature 2012)

    • Medulloblastoma (ICGC, Nature 2012)

    • Medulloblastoma (PCGP, Nature 2012)

    • Multiple Myeloma (Broad, Cancer Cell 2014)

    • Pancreatic Adenocarcinoma (ICGC, Nature 2012)

    • Small Cell Carcinoma of the Ovary (MSKCC, Nature Genetics in press)

    • Small Cell Lung Cancer (CLCGP, Nature Genetics 2012)

    • Small Cell Lung Cancer (Johns Hopkins, Nature Genetics 2012)

    • NCI-60 Cell Lines (NCI, Cancer Res. 2012)

December 9, 2013

  • Added mutation data of 99 bladder cancer samples (BGI, Nature Genetics 2013)

December 6, 2013

  • Data sets matching four recently submitted or published TCGA studies are now available

    • Glioblastoma (Cell 2013)

    • Bladder carcinoma (Nature, in press)

    • Head & neck squamous cell carcinoma (submitted)

    • Lung adenocarcinoma (submitted)

November 8, 2013

  • All TCGA data updated to the Firehose run of September 23, 2013.

  • Updated to the latest COSMIC data (v67).

  • Added mutation data of 792 samples from 9 published cancer studies:

    • Esophageal Adenocarcinoma (Broad, Nature Genetics 2013)

    • Head and Neck Squamous Cell Carcinoma (Broad, Science 2011)

    • Head and Neck Squamous Cell Carcinoma (Johns Hopkins, Science 2011)

    • Kidney Renal Clear Cell Carcinoma (BGI, Nature Genetics 2012)

    • Prostate Adenocarcinoma, Metastatic (Michigan, Nature 2012)

    • Prostate Adenocarcinoma (Broad/Cornell, Nature Genetics 2012)

    • Prostate Adenocarcinoma (Broad/Cornell, Cell 2013)

    • Skin Cutaneous Melanoma (Yale, Nature Genetics 2012)

    • Skin Cutaneous Melanoma (Broad, Cell 2012)

October 21, 2013

  • Improved interface for survival plots, including information on individual samples via mouse-over

  • New fusion glyph in OncoPrints ​FGFR3 fusions in head and neck carcinoma​​

  • Improved cross-cancer query: new alteration frequency histogram (example below - query gene: CDKN2A) and mutation diagram

    ​Cross Cancer Query​

September 9, 2013

  • Updated COSMIC data (v66 Release)

  • Improved / interactive visualization on the "Protein changes" tab

  • Enhanced mutation diagrams: color-coding by mutation time and syncing with table filters

  • Addition of DNA cytoband information in the patient view of copy-number changes

  • OncoPrints now allow the display of an optional track with clinical annotation (Endometrial cancer example below)

    ​Oncoprint with clinical track​

July 25, 2013

  • Multi-gene correlation plots.

  • Variant allele frequency distribution plots for individual tumor samples.

  • Tissue images for TCGA samples in the patient view, via Digital Slide Archive. Example.

July 16, 2013

  • All TCGA data updated to the May Firehose run (May 23, 2013).

    • TCGA Pancreatic Cancer study (provisional) added.

July 4, 2013

  • Improved rendering of mutation diagrams, including ability to download in PDF format.

  • Improved home page: Searchable cancer study & gene set selectors, data sets selector.

June 17, 2013

  • Improved interface for correlation plots, including information on individual samples via mouse-over.

  • Gene Details from Biogene are now available in the Network view.

  • Added mutation and copy number data from a new adenoid cystic carcinoma study: Ho et al., Nature Genetics 2013.

  • Added mutation data from 6 cancer studies.

    • Breast Invasive Carcinoma (Shah et al., Nature 2012)

    • Breast Invasive Carcinoma (Banerji et al., Nature 2012)

    • Breast Invasive Carcinoma (Stephens et al., Nature 2012)

    • Lung Adenocarcinoma (Imielinksi et al., Cell 2012)

    • Lung Adenocarcinoma (Ding et al., Nature 2008)

    • Colorectal Cancer (Seshagiri et al., Nature 2012)

June 4, 2013

  • All TCGA data updated to the April Firehose run (April 21, 2012).

May 14, 2013

  • Added a published TCGA study: Acute Myeloid Leukemia (TCGA, NEJM 2013).

April 28, 2013

  • All TCGA data updated to the March Firehose run (March 26, 2012).

  • mRNA percentiles for altered genes shown in patient view.

April 2, 2013

  • All TCGA data updated to the February Firehose run (February 22, 2012).

March 28, 2013

  • All TCGA data updated to the January Firehose run (January 16, 2012).

  • Data from a new bladder cancer study from MSKCC has been added (97 samples, Iyer et al., JCO in press).

February 16, 2013

  • The cBio Portal now contains mutation data from all provisional TCGA projects. Please adhere to the TCGA publication guidelines when using these and any TCGA data in your publications.

  • All data updated to the October Firehose run (October 24, 2012).

  • Sequencing read counts and frequencies are now shown in the Mutation Details table when available.

  • Improved OncoPrints, resulting in performance improvements.

November 21, 2012

  • Major new feature: Users can now visualize genomic alterations and clinical data of individual tumors, including:

    • Summary of mutations and copy-number alterations of interest

    • Clinical trial information

    • TCGA Pathology Reports

  • New cancer summary view (Example Endometrial Cancer)

  • Updated drug data from KEGG DRUG and NCI Cancer Drugs (aggregated by PiHelper)

October 22, 2012

  • All data updated to the Broad Firehose run from July 25, 2012.

  • COSMIC data added to Mutation Details (via Oncotator).

  • All predicted functional impact scores are updated to Mutation Assessor 2.0.

  • Users can now base queries on genes in recurrent regions of copy-number alteration (from GISTIC via Firehose).

  • The Onco Query Language (OQL) now supports queries for specific mutations or mutation types.

  • Data sets added that match the data of all TCGA publications (GBM, ovarian, colorectal, and lung squamous).

July 18, 2012

  • Mutation data for the TCGA lung squamous cell carcinoma and breast cancer projects (manuscripts in press at Nature).

  • All data updated to the latest Broad Firehose run (May 25, 2012).

  • Drug information added to the network view (via Drugbank).

  • Improved cross-cancer queries: Option to select data types, export of summary graphs.

  • Users can now base queries on frequently mutated genes (from MutSig via Firehose).

May 16, 2012

  • All data updated to the latest Broad Firehose run (March 21, 2012).

  • Extended cross-cancer functionality, enabling users to query across all cancer studies in our database.

  • New "build a case" functionality, enabling users to generate custom case sets, based on one or more clinical attributes.

  • New OncoPrint features, including more compact OncoPrints, and support for RPPA visualization.

February 27, 2012

  • All data updated to the latest Broad Firehose run (January 24, 2012).

  • Validated mutation data for colorectal cancer.

  • New feature: Mutation Diagrams that show mutations in the context of protein domains.

    ​TP53 Mutations in Ovarian Cancer​

January 30, 2012

  • Updated data for several TCGA cancer studies.

  • Some small bug-fixes.

December 22, 2011

  • Fourteen new TCGA cancer studies: This includes complete data for TCGA Colorectal Carcinoma and provisional data for thirteen other cancer types in the TCGA production pipeline. Please note that data from these thirteen new cancer types are provisional, not final and do not yet include mutation data. As per NCI guidelines, preliminary mutation data cannot be redistributed until they have been validated. TCGA​

  • Four new data types:

    • Reverse-phase protein array (RPPA) data.

    • microRNA expression and copy-number (including support for multiple loci)

    • RNA-Seq based expression data.

    • log2 copy-number data.

  • Updated TCGA GBM copy-number, expression, and methylation data.

  • New gene symbol validation service. You can now use gene aliases and/or Entrez Gene IDs within your gene sets.

  • Links to IGV for visualization of DNA copy-number changes.

  • Background information from the Sanger Cancer Gene Census.

  • Two new Tutorials to get you quickly started in using the portal.

November 14, 2011

  • New and improved mutation details, with sorting and filtering capabilities.

  • In collaboration with Bilkent University, we have added a new Network tab to our results pages. The network tab enables users to visualize, analyze and filter cancer genomic data in the context of pathways and interaction networks derived from Pathway Commons.

    ​GBM Network​

September 3, 2011

  • You can now query across different cancer studies (feature available directly from the home page).

  • Our MATLAB CGDS Cancer Genomics Toolbox is now available. The toolbox enables you to download data from the cBio Portal, and import it directly into MATLAB.

  • The code for the cBio Portal has now been fully open sourced, and made available at Google Code. If you would like to join our open source efforts and make the portal even better, drop us an email.

March 2, 2011

New plotting features and other improvements:

  • Correlation plots that show the relationship between different data types for individual genes.

  • Survival analysis - assess survival differences between altered and non-altered patient sets.

  • Updated R Package with support for correlation plots and general improvements for retrieving and accessing data in R data frames.

  • The Web Interface now supports basic clinical data, e.g. survival data.

  • ​Networks for pathway analysis are now available for download.

    ​Survival Analysis​

December 15, 2010

Several new features, including:

  • Redesigned and streamlined user interface, based on user feedback and usability testing.

  • Advanced support for gene-specific alterations. For example, users can now view mutations within TP53, and ignore copy number alterations, or only view amplifications of EGFR, and ignore deletions.

  • Improved performance.

  • ​Frequently Asked Questions document released.

  • Updated Video Tutorial (update: old link no longer functional. Now see: YouTube​

November 4, 2010

  • Enhanced Oncoprints, enabling users to quickly visualize genomic alterations across many cases. Oncoprints now also work in all major browsers, including Firefox, Chrome, Safari, and Internet Explorer.

  • Official release of our Web Interface, enabling programmatic access to all data.

  • Official release of our R Package, enabling programmatic access to all data from the R platform for statistical computing.

    ​OncoPrints​

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Contents
Feb 12, 2020
Feb 6, 2020
Jan 30, 2020
Jan 29, 2020
Dec 19, 2019
Dec 12, 2019
Nov 29, 2019
Nov 22, 2019
Nov 15, 2019
Nov 7, 2019
Oct 30, 2019
October 23, 2019
October 14, 2019
October 11, 2019
October 9, 2019
September 18, 2019
September 6, 2019
August 13, 2019
July 26, 2019
June 19, 2019
June 12, 2019
May 8, 2019
April 26, 2019
March 29, 2019
March 15, 2019
February 22, 2019
February 19, 2019
January 24, 2019
December 17, 2018
October 29, 2018
October 19, 2018
October 17, 2018
August 7, 2018
July 27, 2018
June 20, 2018
May 10, 2018
April 17, 2018
April 05, 2018
March 20, 2018
January 15, 2018
November 20, 2017
October 17, 2017
October 2, 2017
June 26, 2017
May 12, 2017
May 5, 2017
March 28, 2017
Feburary 2, 2017
December 23, 2016
October 7, 2016
July 24, 2016
June 6, 2016
March 31, 2016
January 12, 2016
December 23, 2015
December 1, 2015
November 9, 2015
October 6, 2015
August 21, 2015
June 3, 2015
April 28, 2015
January 20, 2015
January 6, 2015
December 9, 2014
October 24, 2014
August 8, 2014
May 21, 2014
May 12, 2014
March 27, 2014
March 18, 2014
December 9, 2013
December 6, 2013
November 8, 2013
October 21, 2013
September 9, 2013
July 25, 2013
July 16, 2013
July 4, 2013
June 17, 2013
June 4, 2013
May 14, 2013
April 28, 2013
April 2, 2013
March 28, 2013
February 16, 2013
November 21, 2012
October 22, 2012
July 18, 2012
May 16, 2012
February 27, 2012
January 30, 2012
December 22, 2011
November 14, 2011
September 3, 2011
March 2, 2011
December 15, 2010
November 4, 2010