cBioPortal
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2.1 Deployment
2.1.1 Deploy with Docker (Recommended)
2.1.2 Deploy without Docker
2.2 Authorization and Authentication
2.3 Customization
2.4 Integration with Other Webservices
3. cBioPortal Maintenance
4. Development
5.1 Data Loading
5.2 Datasets
6. Web API and Clients
News
Jan 4, 2022
- Added data consisting of 27,447 samples from 10 studies:
- Added TMB (nonsynonymous) scores for all studies. Example: new TMB field for study gbm_cptac_2021 (Details for the calculation can be found HERE)
Nov 12, 2021
- Added data consisting of 3,680 samples from 6 studies:
Nov 3,2021
- New Feature: Add Uniprot topology as a new annotation track on the Mutations Tab of the Results View. Example: EGFR in MSK-IMPACT (2017) cohort
Oct 1, 2021
- New Feature: Arm level Copy Number events are now loaded into cBioPortal using the Categorial Generic Assay Data Type. They can be found in a tab under the Add Charts Button of the Study View Example: Arm Level Data in TCGA PanCancer Atlas
Sep 22, 2021
- Added data consisting of 14,844 samples from 7 studies:
Sep 21, 2021
- Enhancement: Dowloading the Lollipop plot on the Mutations Tab of the Results View will now also include the annotation tracks:
Aug 17, 2021
- New Feature: The Mutations Tab of the Results View can now show exon numbers as an annotation track Example: MET Exon 14 Mutations in MSK-IMPACT (2017) cohort
Aug 10, 2021
- New Feature: Use the filtering capabilities in the Mutations Tab of the Results View to create a custom cohort that one can open directly in the Study View Example: CTNNB1 in MSK-IMPACT (2017) cohort
Jul 27, 2021
- New Feature: Add a custom filter to any column of the Mutations Tab in the Results View Example: CTNNB1 in MSK-IMPACT (2017) cohort
- New Feature: Show detailed descriptions for each annotation source in the header of the the Mutations Table in both the Results View and the Patient View Example link
Jul 6, 2021
- New Feature: Add any clinical data as a column on the Mutations Tab in the Results View Example: EGFR in MSK-IMPACT (2017) cohort
June 23, 2021
- Added data consisting of 1,084 samples from 5 studies:
- Added mass-spec proteome data from CPTAC to Breast Invasive Carcinoma (TCGA, PanCancer Atlas), Ovarian Serous Cystadenocarcinoma (TCGA, PanCancer Atlas) and Colorectal Adenocarcinoma (TCGA, PanCancer Atlas).
- Added mass-spec phosphoproteome site level expression from CPTAC to Breast Invasive Carcinoma (TCGA, PanCancer Atlas) and Ovarian Serous Cystadenocarcinoma (TCGA, PanCancer Atlas).
June 1, 2021
- New Feature: In certain studies where we have the data we show read counts for uncalled mutations on the Patient View Example: A patient in the Glioma (MSK, 2019) cohort
May 10, 2021
- New Feature: Pick color for User Defined Groups Example: Color Bladder Cancer Group in MSK-IMPACT (2017) cohort, implemented by The Hyve.
May 4, 2021
- New Feature: Add more categories of mutations to the Mutations Tab on the Results View, including Driver/VUS, Splice and Structural Variants Example: TP53 alterations in the MSK-IMPACT (2017) cohort
April 21, 2021
- Added data consisting of 4074 samples from 9 studies:
April 20, 2021
- New Feature: Add driver annotations to download tab on Results View Example: RAS/RAF alterations in colorectal cancer
March 30, 2021
- Enhancement: Add 95% Confidence Interval for Survival Plots Example: Altered vs Unaltered EGFR in Lung Cancer
March 11, 2021
- New Feature: Combine different types of alterations in Comparison View Example: Deletions and Truncating events in primary vs metastases or read more on The Hyve's blog
- Enhancement: Improve UI for OncoPrint, aggregating various data modalities in a single add track dropdown button Example: Add clinical, heatmap and treatment response data into the OncoPrint
February 16, 2021
- Enhancement: Show only TCGA PanCancer Atlas Pathways in Results and Patient View to avoid showing many similar pathways Example: Clinvar APC and CTNNB1 alterations in WNT pathway
January 28, 2021
- New Feature: Show ClinVar Interpretation in Mutation tables Example: Clinvar Interpretations in BRCA2
January 12, 2021
- New Feature: Add your own custom data for a sample or patient to use on the study or comparison view Example: Add custom data to three samples and do a comparison
- New Feature: Show the mutations of a patient inside a pathway schematic using PathwayMapper Example: Notch signaling pathway in a prostate cancer patient
- New Feature: Display and compare generic assays, such as microbiome and treatment response, on the study view Example: Prasinovirus microbiome signatures in TCGA
- New Feature: The Plots tab on Results View now allows you to group alterations by Driver and VUS Example: POLE driver mutations vs VUSs against mutation counts in TCGA Colorectal Adenocarcinoma
December 31, 2020
- Added data consisting of 430 samples from 5 studies:
November 3, 2020
October 20, 2020
- Enhancement: Expression tab has now been merged into the Plots tab
October 16, 2020
- Added data consisting of 25,078 samples from 5 studies:
- Added MSI data (MSIsensor from Mariamidze et al. 2018 and MANTIS scores from Roychowdhury et al. 2017) for all 32 TCGA PanCan Atlas Cohorts.
- Added new profile “RNA-Seq V2 expression Z-scores relative to normal samples” for 16 TCGA PanCan Atlas Cohorts. The normals samples RNA-Seq V2 expression data were curated from GDC, and can be downloaded from our Datahub or Data Set page. Example: ERBB2 expression z-scores relative to normal expression
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October 13, 2020
- Enhancement: Study View now allows comparing samples with mutations or copy number alterations in different genes
- New Feature: When treatment timeline is available (e.g. in this study), Study View now allows the selection and comparison of patients treated with specific drugs, or samples sequenced pre or post specific drug treatments
September 30, 2020
- New Feature: Microbiome signature data is available for comparison now. Example: comparing colorectal subtypes for enriched microbiome signatures
September 22, 2020
August 11, 2020
- New Feature: microbiome data of TCGA samples from Poore et al. 2020 are now available for analysis in the OncoPrint and Plots tabs. Example: Orthohepadnavirus across TCGA cancers
- New Feature: You can now compare DNA Methylation data between groups using the Comparison feature. Example: Comparing DNA methylation levels between samples with high vs low BRCA1 expression
- Added data consisting of 513 samples from 3 studies:
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July 21, 2020
- New Feature: The Mutations tab now has the option to show mutation effects for different transcripts / isoforms. Note that some annotation features are only available for the canonical isoform. example
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June 11, 2020
- Added data consisting of 267 samples from 2 studies:
June 9, 2020
- Enhancement: Mutational spectrum data can be downloaded from OncoPrint
June 2, 2020
- Enhancement: Pediatric cancer studies are now grouped and highlighted in the query page
May 6, 2020
- Added data consisting of 574 samples from 3 studies:
- Updated one study:
April 24, 2020
- New Feature: Add a new chart on the Study View for selecting samples based on pre-defined case lists:
April 10, 2020
- New Feature: Make cohorts on the Study View using continuous molecular profiles of one or more gene(s), such as mRNA expression, methylation, RPPA and continuous CNA. example
Combine this with the group comparison feature to compare e.g. all quartiles of expression:
- New Feature: Annotate mutations using the Mutation Mapper Tool on the GRCh38 reference genome:
April 3, 2020
- New Feature: Extended the Comparison tab to support the comparison of altered samples per gene or alteration. This example query compares NSCLC patients with 1) both mutated and amplified EGFR, 2) mutated EGFR only, and 3) amplified EGFR only.
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March 27, 2020
March 20, 2020
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March 18, 2020
- Added data consisting of 1,393 samples from 3 studies:
March 3, 2020
- New Feature: Added Pathways tab to the Results View page, which visualizes the alteration frequencies of genes in pathways of interest. The pathways are pulled from https://www.pathwaymapper.org and shown in a read only view. One can edit these pathways in the PathwayMapper editor. For more information see the tutorial.
February 12, 2020
- Added data consisting of 1,605 samples from 3 studies:
February 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:
- 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.
January 30, 2020
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- Enhancement: Add a pencil button near gene list in results page which opens interface for quickly modifying the oql of the query:
January 29, 2020
- Added data consisting of 197 samples from 2 studies:
December 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.
December 12, 2019
- Enhancement: Add Count Bubbles to Oncoprint Toolbar
November 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.
November 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
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November 15, 2019
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- Enhancement: global settings for query session
November 7, 2019
- Added data consisting of 212 samples from 3 studies:
October 30, 2019
- Added data consisting of 178 samples from 2 studies:
October 23, 2019
October 14, 2019
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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:
Results page:
Note that as before one can always download the full raw data on the Data Sets page or from Datahub.
October 9, 2019
- Added data consisting of 2725 samples from 4 studies:
- Updated Esophageal Carcinoma (TCGA, Nature 2017) with addition of CNA data for Esophageal Squamous Cell Carcinoma cases 90 samples.
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
- Added data consisting of 1216 samples from 3 studies:
August 13, 2019
- Added data consisting of 295 samples from 3 studies:
July 26, 2019
- Added data consisting of 35 samples from 1 study:
- Added Hypoxia data for:
July 24, 2019
- Added data consisting of 151 samples from 1 study:
July 13, 2019
- Public Release 6.1 of AACR Project GENIE:
- The sixth data set, GENIE 6.0-public, was released in early July 2019. A patch to GENIE 6.0-public, GENIE 6.1-pubic, was subsequently released on July 13, 2019. The combined data set now includes nearly 70,000 de-identified genomic records collected from patients who were treated at each of the consortium's participating institutions, making it among the largest fully public cancer genomic data sets released to date. The combined data set now includes data for nearly 80 major cancer types, including data from nearly 11,000 patients with lung cancer, greater than 9,700 patients with breast cancer, and nearly 7,000 patients with colorectal cancer.
- More detailed information can be found in the AACR GENIE Data Guide. In addition to accessing the data via the cBioPortal, users can download the data directly from Sage Bionetworks. Users will need to create an account for either site and agree to the terms of access.
July 2, 2019
- Added data consistng of 785 samples from 4 studies:
June 19, 2019
- New Feature: Show Genome Aggregation Database (gnomAD) population frequencies in the mutations table - see example:
June 12, 2019
- Added data of 1350 samples from 3 studies:
- Added survival data for TCGA PanCan Atlas Cohorts (>10,000 samples across 33 tumor types).
June 7, 2019
- New Group Comparison Feature: Compare clinical and genomic features of user-defined groups of samples/patients. View Tutorial
May 8, 2019
April 26, 2019
- Added data of 568 samples from 4 studies:
March 29, 2019
- New Feature: Use the new quick search tab on the homepage to more easily navigate to a study, gene or patient:
March 15, 2019
- Added data of 338 samples from 4 studies:
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
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February 19, 2019
- Improved Copy-Number Segments tab on the Results page
- New feature: OncoKB and Cancer Hotspots tracks in the Mutations tab on the Results page
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January 24, 2019
- Added data of 2328 samples from 8 studies:
January 10, 2019
- cBioPortal now supports queries for driver mutations, fusions and copy number alterations as well as germline/somatic mutations using Onco Query Language (OQL) -- see example
- A new tutorial explores OQL and provides examples of how OQL can be a powerful tool to refine queries.
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! 🎉🎉🎉
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
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October 19, 2018
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October 17, 2018
- Added data of 3578 samples from 8 studies:
August 20, 2018
- Now you can log in on the public cBioPortal with your Google account and save your virtual studies for quick analysis.
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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.
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July 27, 2018
- Added data of 2787 samples from 10 studies:
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.
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May 10, 2018
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April 17, 2018
- Added data of 3732 samples from 4 TARGET studies:
- Added data of 3416 samples from 10 published studies:
April 5, 2018
- Added data from the TCGA PanCanAtlas project with >10,000 samples from 33 tumor types: