cBioPortal protocols

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cBioPortal specifications

Information


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

Maintainer


  • person_outline Ethan Cerami <>

Publications for cBioPortal

cBioPortal in pipelines

 (62)
2018
PMCID: 5743717
PMID: 29290775
DOI: 10.7150/jca.21925

[…] of egf-treated data normalized to the input control and untreated data normalized to the input control., tcga rna expression data (rna seq v2 rsem) and survival data were queried and downloaded via cbioportal (http://www.cbioportal.org/), followed by data processing in r environment. the cancer types and corresponding sample size for 17 datasets were listed in table . for evaluating […]

2018
PMCID: 5839398
PMID: 29515767
DOI: 10.18632/oncotarget.24188

[…] by a > ×0.7 log2 ratio with a length less than 10 mb were considered of interest for the current study., to annotated the pathogenicity of the erbb2 mutations, we have used snpeff (v4.0e) and the cbioportal annotation tool []. only pathogenic variants detected in the tumor were selected to orientate the patients to her2 inhibitors. we have mapped the mutations on a schematic structure […]

2018
PMCID: 5872397
PMID: 29587824
DOI: 10.1186/s13059-018-1420-6

[…] a pearson correlation p < 0.05 and log2-transformed expression fold change between the highest and lowest sample > 0.5. for tcga gbm data, the co-expression gene list was acquired from cbioportal using a pearson correlation > 0.3 or < − 0.3. mirna targeting and network analysis was performed with mirdb (http://www.mirdb.org/mirdb/) and mirnet (http://www.mirnet.ca/) […]

2018
PMCID: 5882046
PMID: 29558872
DOI: 10.1177/1533033818764499

[…] toolkit (webgestalt, http://www.webgestalt.org/). additionally, genes associated with nk cell-mediated cytotoxicity were further introduced into the cbio cancer genomics portal (cbioportal, http://www.cbioportal.org/); the breast invasive carcinoma (tcga, provisional) was selected and the messenger rna (mrna) expression data with a z score threshold of ± 2.0 was used. […]

2018
PMCID: 5886988
PMID: 29367767
DOI: 10.1038/s41388-017-0099-6

[…] antibody specificity was assessed using kmt2d wild type and homozygote-mutant cell lines. no expression of kmt2d was detected in kmt2d-mutant cells., r code use for accessing tcga data from the cbioportal server (‘tcgaretriever’ package) and for analyzing and extracting mutational signatures (‘mutsignatures’ package) is available at the comprehensive r archive network […]


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cBioPortal in publications

 (1440)
PMCID: 5954021
PMID: 29765039
DOI: 10.1038/s41467-018-04313-6

[…] (pierce) according to the manufacturer’s instruction., 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 […]

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

[…] 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., all rnaseq data were log-transformed. significantly related genes with ptpn2 expression […]

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

[…] 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 […]

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

[…] 3.4.2 and its packages genomicalignments (1.12.2) and genomicranges (1.28.4) from data downloaded through the gdc portal. expression data of the tumors from uvm_1 and gbm_4 was explored through the cbioportal. effect of splice mutations was predicted on the major transcript with the alamut visual software (interactive software, rouen, france), which contains the algorithms splicesitefinder, […]

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

[…] with accession number e-mtab-5552 (450k methylation)., 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)., […]


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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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