News
Added data consisting of 1084 samples from 5 studies:
Intrahepatic Cholangiocarcinoma (MSK, 2020) 219 samples
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).
New Feature: Pick color for User Defined Groups Example: Color Bladder Cancer Group in MSK-IMPACT (2017) cohort, implemented by The Hyve.
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
Added data consisting of 4074 samples from 9 studies:
Metaplastic Breast Cancer (MSK, 2021) 19 samples
Lung Adenocarcinoma (MSKCC, 2020) 604 samples
Cutaneous Squamous Cell Carcinoma (UCSF, 2021) 105 samples
MSK-IMPACT and MSK-ACCESS Mixed Cohort (MSK, 2021) 1446 samples
Melanoma (MSKCC, 2018) 720 samples
Cholangiocarcinoma (ICGC, Cancer Discov 2017) 489 samples
Esophageal/Stomach Cancer (MSK, 2020) 487 samples
Retinoblastoma (MSK, Cancers 2021) 83 samples
New Feature: Add driver annotations to download tab on Results View Example: RAS/RAF alterations in colorectal cancer
Enhancement: Add 95% Confidence Interval for Survival Plots Example: Altered vs Unaltered EGFR in Lung Cancer
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
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
New Feature: Show ClinVar Interpretation in Mutation tables Example: Clinvar Interpretations in BRCA2
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
Added data consisting of 430 samples from 5 studies:
Mixed cfDNA (MSKCC, 2020) 229 samples
Metastatic Melanoma (DFCI, Nature Medicine 2019) 144 samples
Lung Cancer (SMC, Cancer Research 2016) 22 samples
Added survival data to Breast Cancer (METABRIC, Nature 2012 & Nat Commun 2016)
Enhancement: upgraded the Genomic Evolution tab in Patient View with timeline Example
Enhancement: Expression tab has now been merged into the Plots tab
Added data consisting of 25,078 samples from 5 studies:
Melanomas (TCGA, Cell 2015) 359 samples
Retinoblastoma cfDNA (MSKCC 2020) 14 samples
Bladder Cancer (MSK/TCGA, 2020) 476 samples
Cancer Therapy and Clonal Hematopoiesis (MSK, 2020) 24,146 samples
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
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
New Feature: Microbiome signature data is available for comparison now. Example: comparing colorectal subtypes for enriched microbiome signatures
Enhancement: The timeline feature in Patient View has been refactored with an improved UI. Example
Enhancement: Logrank p-values are now provided for all survival analysis (previously only availalbe when comparing two groups). Example
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:
Breast Cancer (SMC 2018) 187 samples
Germ Cell Tumors and Shared Leukemias (MSK 2020) 21 samples
Lung Adenocarcinoma (OncoSG, Nat Genet 2020) 305 samples
Added RPPA data in addition to the microbiome data for 31 TCGA Pancan studies (except LAML)
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
Enhancement: The Plots tab is now supported in multi-study queries. example
New Feature: You can now share custom groups in the Study View example
Added data consisting of 267 samples from 2 studies:
Gastric Cancer (OncoSG, 2018) 147 samples
120 ctDNA samples added to Non-Small Cell Lung Cancer (TRACERx, NEJM & Nature 2017) 447 samples
Enhancement: using OQL to query for mutations based on a protein position range. [example](https://www.cbioportal.org/results/mutations?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=msk_impact_2017&case_set_id=msk_impact_2017_cnaseq&data_priority=0&gene_list=TP53%253AMUT_(95-288*)&geneset_list= &genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=msk_impact_2017_cna&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=msk_impact_2017_mutations&profileFilter=0&tab_index=tab_visualize)
New Feature: you can now send the OncoPrint data to the OncoPrinter tool for customization.
Enhancement: Mutational spectrum data can be downloaded from OncoPrint
Enhancement: Pediatric cancer studies are now grouped and highlighted in the query page
Added data consisting of 574 samples from 3 studies:
Updated one study:
Expression data was added to The Metastatic Breast Cancer Project (Provisional, February 2020).
New Feature: Add a new chart on the Study View for selecting samples based on pre-defined case lists:
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](https://www.cbioportal.org/study/summary?id=brca_tcga#filterJson={"genomicDataFilters":[{"hugoGeneSymbol":"ERBB2","profileType":"mrna_median_Zscores","values":[{"start":1.5,"end":2},{"start":2,"end":2.5},{"start":2.5,"end":3},{"start":3,"end":3.5},{"start":3.5,"end":4},{"start":4}]}],"genomicProfiles":[["mrna_median_Zscores"]],"studyIds":["brca_tcga"]})
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:
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.
Enhancement: User selections in the Plots tab are now saved in the URL. example
New Feature: Added table of data availability per profile in the Study View. example
Enhancement: Extended Survival Analysis to support more outcome measures. example
Added data consisting of 1,393 samples from 3 studies:
Glioma (MSKCC, Clin Cancer Res 2019) 1,004 samples
Mixed cfDNA (MSK, Nature Medicine 2019) 248 samples
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.
Added data consisting of 1,605 samples from 3 studies:
Tumors with TRK fusions (MSK, 2019) 106 samples
Lymphoma Cell Lines (MSKCC, 2020) 34 samples
Prostate Adenocarcinoma (MSKCC, 2020) 1,465 samples
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.
Read more about the v3.2.2 release here
Enhancement: Show HGVSg in mutations table and linkout to Genome Nexus:
Enhancement: Add a pencil button near gene list in results page which opens interface for quickly modifying the oql of the query:
See more updates here
Added data consisting of 197 samples from 2 studies:
Bladder/Urinary Tract Cancer (MSK, 2019) 78 samples
Upper Tract Urothelial Carcinoma (MSK, 2019) 119 samples
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
Enhancement: Add Count Bubbles to Oncoprint Toolbar
See more updates here
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
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
Enhancement: heatmap tracks in OncoPrint now has separate headers and sub-menus. example
Enhancement: global settings for query session
Added data consisting of 212 samples from 3 studies:
Metastatic Melanoma (DFCI, Science 2015) 110 samples
Melanoma (MSKCC, NEJM 2014) 64 samples
Metastatic Melanoma (UCLA, Cell 2016) 38 samples
Added data consisting of 178 samples from 2 studies:
Enhancement: Quick example links in Plots tab. example
New Feature: Fusion Genes table in
Study View. example
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.
Added data consisting of 2725 samples from 4 studies:
Cancer Cell Line Encyclopedia (Broad, 2019) 1739 samples
Chronic Lymphocytic Leukemia (Broad, Nature 2015) 537 samples
Rectal Cancer (MSK,Nature Medicine 2019) 339 samples
Colon Cancer (CPTAC-2 Prospective, Cell 2019) 110 samples
Updated Esophageal Carcinoma (TCGA, Nature 2017) with addition of CNA data for Esophageal Squamous Cell Carcinoma cases 90 samples.
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.
Added data consisting of 1216 samples from 3 studies:
Breast Cancer (MSKCC, 2019) 70 samples
Brain Tumor PDXs (Mayo Clinic, 2019)97 samples
Adenoid Cystic Carcinoma Project (2019) 1049 samples
Added data consisting of 295 samples from 3 studies:
Non-small cell lung cancer (MSK, Science 2015) 16 samples
Prostate Cancer (MSK, 2019) 18 samples
Added data consisting of 35 samples from 1 study:
Added Hypoxia data for:
Uterine Corpus Endometrial Carcinoma (TCGA, PanCancer Atlas)
July 24, 2019
Added data consisting of 151 samples from 1 study:
Myeloproliferative Neoplasms (CIMR, NEJM 2013) 151 samples
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.
For frequently asked questions, visit the AACR FAQ page.
July 2, 2019
Added data consistng of 785 samples from 4 studies:
Non-Small Cell Lung Cancer (TRACERx, NEJM 2017) 327 samples
Basal Cell Carcinoma (UNIGE, Nat Genet 2016) 293 samples
Colon Adenocarcinoma (CaseCCC, PNAS 2015) 29 samples
New Feature: Show Genome Aggregation Database (gnomAD) population frequencies in the mutations table - see example:
Added data of 1350 samples from 3 studies:
Pheochromocytoma and Paraganglioma (TCGA, Cell 2017) 178 samples
Metastatic Solid Cancers (UMich, Nature 2017) 500 samples
Acute Myeloid Leukemia (OHSU, Nature 2018) 672 samples
Added survival data for TCGA PanCan Atlas Cohorts (>10,000 samples across 33 tumor types).
Added hypoxia data for Bladder Urothelial Carcinoma (TCGA, PanCancer Atlas)
June 7, 2019
New Group Comparison Feature: Compare clinical and genomic features of user-defined groups of samples/patients. View Tutorial
Added data of 568 samples from 4 studies:
Histiocytosis Cobimetinib (MSK, Nature 2019) 52 samples
New Feature: Use the new quick search tab on the homepage to more easily navigate to a study, gene or patient:
Added data of 338 samples from 4 studies:
Adenoid Cystic Carcinoma (MGH, Nat Gen 2016) 10 samples
Gallbladder Cancer (MSK, Cancer 2018) 103 samples
Adult Soft Tissue Sarcomas (TCGA, Cell 2017) 206 samples
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
Improved Copy-Number Segments tab on the Results page
New feature: OncoKB and Cancer Hotspots tracks in the Mutations tab on the Results page
Added data of 2328 samples from 8 studies:
Uveal Melanoma (QIMR, Oncotarget 2016) 28 samples
TMB and Immunotherapy (MSKCC, Nat Genet 2019) 1661 samples
Glioma (MSK, 2018) 91 samples
Hepatocellular Carcinoma (MSK, Clin Cancer Res 2018) 127 samples
MSK Thoracic PDX (MSK, Provisional) 139 samples
Cholangiocarcinoma (MSK, Clin Cancer Res 2018) 195 samples
Updated data for The Metastatic Breast Cancer Project (Provisional, October 2018) 237 samples
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.
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! 🎉🎉🎉
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
Support selection of transcript of interest in the MutationMapper tool via Genome Nexus.
Added data of 3578 samples from 8 studies:
Rhabdoid Cancer (BCGSC, Cancer Cell 2016) 40 samples
Diffuse Large B-Cell Lymphoma (Duke, Cell 2017) 1001 samples
Diffuse Large B cell Lymphoma (DFCI, Nat Med 2018) 135 samples
Uterine Clear Cell Carcinoma (NIH, Cancer 2017) 16 samples
Endometrial Cancer (MSK, 2018) 197 samples
Breast Cancer (MSK, Cancer Cell 2018) 1918 samples
MSS Mixed Solid Tumors (Van Allen, 2018) 249 samples
Updated data for The Angiosarcoma Project (Provisional, September 2018) 48 samples
Now you can log in on the public cBioPortal with your Google account and save your virtual studies for quick analysis.
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.
Added data of 2787 samples from 10 studies:
Mixed Tumors (PIP-Seq 2017) 103 samples
Pediatric Neuroblastoma (TARGET, 2018) 1089 samples
Non-Hodgkin Lymphoma (BCGSC, Nature 2011) 14 samples
Chronic lymphocytic leukemia (ICGA, Nat 2011) 105 samples
Neuroblastoma (Broad Institute 2013) 240 samples
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
Enhanced OncoPrint to show germline mutations -- see example
Added data of 3732 samples from 4 TARGET studies:
Pediatric Acute Myeloid Leukemia (TARGET, 2018) 1025 samples
Pediatric Rhabdoid Tumor (TARGET, 2018) 72 samples
Pediatric Wilms' Tumor (TARGET, 2018) 657 samples
Added data of 3416 samples from 10 published studies:
Prostate Adenocarcinoma (EurUrol, 2017) 65 samples
Non-Small Cell Lung Cancer (MSK, JCO 2018) 240 samples
Small-Cell Lung Cancer (Multi-Institute 2017) 20 samples
Colorectal Cancer (MSK, Cancer Cell 2018) 1134 samples
Bladder Cancer (TCGA, Cell 2017) 413 samples
Added data from the TCGA PanCanAtlas project with >10,000 samples from 33 tumor types:
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.
The fifth phase of the cBioPortal architectural upgrade is now complete: The OncoPrint and Survival tabs have been moved to the new architecture.
You can now combine multiple studies and view them on the study summary page. Example: liver cancer studies
You can now bookmark or share your selected samples as virtual studies with the share icon on the study summary page. Example: a virtual study of breast tumors
Cross-study query reimplemented: Now you can view an OncoPrint of multiple studies. Example: querying NSCLC tumors from 5 studies
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.
Added data of 1646 samples from 7 published studies:
Updated data for MSK-IMPACT Clinical Sequencing Cohort (MSK, Nat Med 2017) with overall survival data.
August 3, 2017
The third phase of the cBioPortal architectural upgrade is now complete: The Mutations tab now has a fresh look and faster performance -- see example
Variant interpretations from the CIViC database are now integrated into the annotation columns on the Mutations tab and in the patient view pages
New summary graph for all cancer studies and samples on the front page
The second phase of the cBioPortal architectural upgrade is now complete: The query interface now has a fresh look and faster performance.
Added data of 12,211 samples from 11 published studies:
MSK-IMPACT Clinical Sequencing Cohort (MSK, Nat Med 2017) 10,945 samples
Hepatocellular Carcinomas (INSERM, Nat Genet 2015) 243 samples
Medulloblastoma (Sickkids, Nature 2016) 46 samples
Ampullary Carcinoma (Baylor, Cell Reports 2016) 160 samples
First phase of cBioPortal architectural upgrade complete: Patient view now has fresh look and faster performance. example
New features:
Per-sample mutation spectra are now available in OncoPrints -- see example
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
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
New features:
Heat map visualization of gene expression data in the OncoPrint
Heat map visualization of gene expression data in the Study View page connecting to MDACC's TCGA Next-Generation Clustered Heat Map Compendium
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
Copy number segments visualization directly in the browser in a new CN Segments tab via IGV.js
Improvements:
Improved cancer study view page (bug fixes and increased performance)
Added data of 4,375 samples from 21 published studies:
Adenoid Cystic Carcinoma (MDA, Clin Cancer Res 2015) 102 samples
Adenoid Cystic Carcinoma (Sanger/MDA, JCI 2013) 24 samples
Breast Cancer (METABRIC, Nat Commun 2016) 1980 samples
Chronic Lymphocytic Leukemia (Broad, Cell 2013) 160 samples
Chronic Lymphocytic Leukemia (IUOPA, Nature 2015) 506 samples
Colorectal Adenocarcinoma (DFCI, Cell Reports 2016) 619 samples
Diffuse Large B-Cell Lymphoma (Broad, PNAS 2012) 58 samples
Insulinoma (Shanghai, Nat Commun 2013) 10 samples
Mantle Cell Lymphoma (IDIBIPS, PNAS 2013) 29 samples
Myelodysplasia (Tokyo, Nature 2011) 29 samples
Neuroblastoma (Broad, Nat Genet 2013) 56 samples
Pancreatic Adenocarcinoma (QCMG, Nature 2016) 383 samples
New TCGA study:
Pan-Lung Cancer (TCGA, Nat Genet 2016) 1144 samples
Updated TCGA provisional studies
updated to the Firehose run of January 28, 2016
RPPA data updated with the latest data from MD Anderson
OncoTree codes assigned per sample
New features:
Annotation of mutation effect and drug sensitivity on the Mutations tab and the patient view pages (via OncoKB)
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
New features:
Visualization of "Enrichments Analysis" results via volcano plots
Improved performance of the cross cancer expression view by switching to Plot.ly graphs
Improvements to the "Clinical Data" tab on the study view page
More customization options for the cross-cancer histograms
Performance improvements in the study view and query result tabs
Added data of 1235 samples from 3 published studies:
New features:
Visualization of multiple samples in a patient
Visualization of timeline data of a patient (example)
All TCGA data updated to the latest Firehose run of August 21, 2015
Added data of 650 samples from 10 published studies:
All mutation data mapped to UniProt canonical isoforms
New features:
Visualization of RNA-seq expression levels across TCGA studies (cross-cancer queries)
Selection of genes in the study view to initiate queries
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
New feature: Annotated statistically recurrent hotspots, via new algorithm by Chang et al. 2015</br>
New features:
Links to MyCancerGenome.org for mutations
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)
Added data of 763 samples from 12 published studies:
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.
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.
New features:
Redesigned query interface to allow selecting multiple cancer studies
Redesigned Plots tab
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
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.
New TCGA data:
Added complete and up-to-date clinical data for all TCGA provisional studies
All TCGA data updated to the Firehose run of July 15, 2014
New TCGA provisional studies: Esophageal cancer, Pheochromocytoma and Paraganglioma (PCPG)
New published TCGA studies: Thyroid Cancer and Kidney Chromophobe
Added data of 172 samples from 4 published studies:
New features:
Redesigned Mutual Exclusivity tab
Added correlation scores for scatter plots on the Plots tab
Download links to GenomeSpace
Added data of 885 samples from 11 published studies:
Released two new tools
Oncoprinter lets you create Oncoprints from your own, custom data
MutationMapper draws mutation diagrams (lollipop plots) from your custom data
All TCGA data updated to the Firehose run of April 16, 2014
Improved study summary page including survival analysis based on clinical attributes
e.g. TCGA Endometrial Cancer cohort
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
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)
Added mutation data of 99 bladder cancer samples (BGI, Nature Genetics 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)
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)
Improved interface for survival plots, including information on individual samples via mouse-over
New fusion glyph in OncoPrints
Improved cross-cancer query: new alteration frequency histogram (example below - query gene: CDKN2A) and mutation diagram
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)
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.
All TCGA data updated to the May Firehose run (May 23, 2013).
TCGA Pancreatic Cancer study (provisional) added.
Improved rendering of mutation diagrams, including ability to download in PDF format.
Improved home page: Searchable cancer study & gene set selectors, data sets selector.
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)
All TCGA data updated to the April Firehose run (April 21, 2012).
Added a published TCGA study: Acute Myeloid Leukemia (TCGA, NEJM 2013).
All TCGA data updated to the March Firehose run (March 26, 2012).
mRNA percentiles for altered genes shown in patient view.
All TCGA data updated to the February Firehose run (February 22, 2012).
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).
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.
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)
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).
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).
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.
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.
Updated data for several TCGA cancer studies.
Some small bug-fixes.
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.
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.
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.
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.
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.
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
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.
