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cBioPortal specifications


Unique identifier OMICS_03396
Name cBioPortal
Interface Web user interface, Application programming interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Ethan Cerami

Publications for cBioPortal

cBioPortal citations


Estrogen related receptor gamma functions as a tumor suppressor in gastric cancer

Nat Commun
PMCID: 5954140
PMID: 29765046
DOI: 10.1038/s41467-018-04244-2

[…] ressors, and deregulation (methylation or mutation) of TFs leads to tumorigenesis. Recent genomic analysis from public databases suggests that ESRRG is not frequently methylated or mutated in GC (www.cbioportal.org). Thus, the decreased levels of ESRRG in GC are likely to be through a mechanism that is distinct from conventional tumor suppressive TFs. Thus, the mechanisms underlying the deregulati […]


Molecular and clinical characterization of PTPN2 expression from RNA seq data of 996 brain gliomas

PMCID: 5953404
PMID: 29764444
DOI: 10.1186/s12974-018-1187-4
call_split See protocol

[…] q data of 325 patients with glioma (World Health Organization (WHO) grades II–IV) from the CGGA dataset, have been described in our previous study []. Besides, data from TCGA were downloaded from the cBioPortal (http://www.cbioportal.org/), and 671 gliomas (WHO grades II–IV) were analyzed in this study. […]


STT3 dependent PD L1 accumulation on cancer stem cells promotes immune evasion

Nat Commun
PMCID: 5954021
PMID: 29765039
DOI: 10.1038/s41467-018-04313-6
call_split See protocol

[…] The mRNA expression (RNA Seq V2 RSEM) database of TCGA Breast Invasive Carcinoma (n = 1100) was downloaded from the open-source resource of the cBioPortal for Cancer Genomics [http://www.cbioportal.org/index.do]. The log2 ratio of downloaded data was determined using Cluster 3.0 software [http://bonsai.hgc.jp/~mdehoon/software/cluster/softwar […]


High‐throughput discovery of functional disordered regions: investigation of transactivation domains

Mol Syst Biol
PMCID: 5949888
PMID: 29759983
DOI: 10.15252/msb.20188190

[…] e W30R in EKLF4 (allele frequency in the human population of 1.3 × 10−5; gnomAD database) and the E135K mutation in ESX, which is prevalent in esophageal adenocarcinoma (allele frequency of 0.37 from cBioPortal), may lead to loss of TAD activity in these transcription factors (). Thus, IDR‐Screen can be a powerful framework to screen and infer the functional impact of a large number of naturally o […]


Molecular, Pathological, Radiological, and Immune Profiling of Non brainstem Pediatric High Grade Glioma from the HERBY Phase II Randomized Trial

Cancer Cell
PMCID: 5956280
PMID: 29763623
DOI: 10.1016/j.ccell.2018.04.004

[…] Curated gene-level copy number, mutation data and RNAseq data are provided as part of the paediatric-specific implementation of the cBioPortal genomic data visualization portal (pedcbioportal.org). Raw data files are also made available through the Cavatica NIH-integrated cloud platform (cavatica.org). […]


Outlier response to anti PD1 in uveal melanoma reveals germline MBD4 mutations in hypermutated tumors

Nat Commun
PMCID: 5951831
PMID: 29760383
DOI: 10.1038/s41467-018-04322-5

[…] .sourceforge.net/; ANNOVAR, http://annovar.openbioinformatics.org/en/latest/; cosmic80, cancer.sanger.ac.uk; GDC portal, https://portal.gdc.cancer.gov; ExAC database, http://exac.broadinstitute.org/; cbioportal, http://www.cbioportal.org/. […]


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cBioPortal institution(s)
Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA; Computer Engineering Department, Bilkent University, Ankara, Turkey; Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden; Blueprint Medicines, Cambridge, MA, USA
cBioPortal funding source(s)
Supported by NCI as part of the TCGA Genome Data Analysis Center grant, NCI-U24CA143840, and NCI-R21CA135870, a Stand Up To Cancer Dream Team Translational Research Grant, a Program of the Entertainment Industry Foundation (SU2C-AACR-DT0209), the National Resource for Network Biology (NIH National Center for Research Resources grant numbers P41 RR031228 and GM103504), the NIH NCI R01 CA132744 and the Starr Cancer Consortium (I5-A500).

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