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The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data
Open accessAbstract
The cBio Cancer Genomics Portal (http://cbioportal.org) is an open-access resource for interactive exploration of multidimensional cancer genomics data sets, currently providing access to data from more than 5,000 tumor samples from 20 cancer studies. The cBio Cancer Genomics Portal significantly lowers the barriers between complex genomic data and cancer researchers who want rapid, intuitive, and high-quality access to molecular profiles and clinical attributes from large-scale cancer genomics projects and empowers researchers to translate these rich data sets into biologic insights and clinical applications. Cancer Discov; 2(5); 401–4. ©2012 AACR.
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In the citing paper
“Second, cBioPortal and COSMIC are primarily focused on patient tumour genomic data.”
From Cell Model Passports-a hub for clinical, genetic and functional datasets of preclinical cancer models (2019) · cites this paper as [36]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“Publicly available gene expression data from a matched cohort established previously59 or mCRPC was downloaded from cBioportal (20 May 2021)94–96.”
From Genome-scale CRISPR screens identify PTGES3 as a direct modulator of androgen receptor function in advanced prostate cancer (2025) · cites this paper as [95]
The check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“IMP2 is genomically altered in over 2% of all cancers, which is above the baseline of random alterations in the average passenger genes (Figure 5A) [77,78,79].”
From IMPlications of IMP2 in RNA Biology and Disease (2025) · cites this paper as [77]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“Genomic amplifications creating extra copies of IGF2BP2 occur in 9% of lung cancers (Figure 5A) [77,78,79].”
From IMPlications of IMP2 in RNA Biology and Disease (2025) · cites this paper as [77]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“KRAS mutations are implicated in 25–30% of all human cancers, about 19% of non-small cell lung cancers (NSCLCs), about 40% of colorectal cancers (CRCs), and about 73% of pancreatic ductal adenocarcinoma (PDAC) cases (Figure 1) [1,2].”
From KRAS: Biology, Inhibition, and Mechanisms of Inhibitor Resistance (2024) · cites this paper as [1]
Experimental — accuracy not yet measured
The check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“TP53 is deregulated in 22% of GBMs, while ARF, MDM2, and MDM4 are deregulated in 61%, 10%, and 10% of GBMs, respectively (Figure 1) [22,23].”
From The p53 Pathway in Glioblastoma (2018) · cites this paper as [22]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“The most frequently deregulated component of the p53 pathway is a homozygous deletion of the CDKN2A/ARF locus, which occurs in ~60% of all GBM cases (Figure 1) [22,23].”
From The p53 Pathway in Glioblastoma (2018) · cites this paper as [22]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“in patients with HCC, high PROX1 expression or chromosomal amplifications including PROX1 were both associated with increased survival25–32”
From Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis (2025) · cites this paper as [26]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“in patients with HCC, high PROX1 expression or chromosomal amplifications including PROX1 were both associated with increased survival25–32”
From Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis (2025) · cites this paper as [26]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“The prevalence of STAT3 overactivation in cancer cannot be explained by mutational activation of STAT3 because somatic mutation of the STAT3 gene in cancer is rare (1.08%; 54/4980 tumors analyzed to date by whole exome sequencing by The Cancer Genome Atlas).38”
From Critical analysis of the potential for targeting STAT3 in human malignancy (2013) · cites this paper as [38]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“It is an important tumour suppressor gene mutated in 6% of colorectal cancers (CRCs), and germline variants in PTEN are causative of PTEN hamartoma tumour syndrome (Hobert and Eng, 2009; Cerami et al., 2012).”
From Efficient genetic editing of human intestinal organoids using ribonucleoprotein-based CRISPR (2023) · cites this paper as Cerami et al., 2012
Experimental — accuracy not yet measuredIn the citing paper
“We note that the region of BRCA1 (amino acid residues 758-1064) that harbors the RAD51 interaction domain17 is frequently mutated in cancer (cBioPortal for Cancer Genomic)44,45”
From BRCA1–BARD1 promotes RAD51-mediated homologous DNA pairing (2017) · cites this paper as [44]
In the citing paper
“Despite being the most frequently altered oncogenic protein in solid tumours, KRAS has historically been considered ‘undruggable’”
From The current state of the art and future trends in RAS-targeted cancer therapies (2022) · cites this paper as [17]
In the citing paper
“each dataset indicates that ~20% of all malignancies have a RAS abnormality. Overall, ~17% of solid tumours have KRAS mutations, including ~90% of pancreatic, ~50% of colon and ~25% of lung adenocarcinomas16,17”
From The current state of the art and future trends in RAS-targeted cancer therapies (2022) · cites this paper as [17]
In the citing paper
“KRAS mutations predominate in NSCLCs, accounting for ~78% of all RAS mutations found in such tumours17. The activating missense KRAS mutations that occur in ~25% of NSCLCs19–23 are typically mutually exclusive with other clinically actionable driver mutations, such as those in EGFR, BRAF and ALK24.”
From The current state of the art and future trends in RAS-targeted cancer therapies (2022) · cites this paper as [17]
In the citing paper
“approximately one in seven of all human cancers harbor KRAS (Kirsten rat sarcoma virus) alterations”
From Expanding the Reach of Precision Oncology by Drugging All KRAS Mutants (2022) · cites this paper as [4]
In the citing paper
“KRAS is the most frequently mutated oncogene”
From Expanding the Reach of Precision Oncology by Drugging All KRAS Mutants (2022) · cites this paper as [4]
In the citing paper
“Based on non-small cell lung cancer datasets within cBioPortal, the landscape of KRAS G12C mutated tumors includes a complex landscape of co-altered genes (Fig. 3)25,26.”
From Selective KRAS G12C inhibitors in non-small cell lung cancer: chemistry, concurrent pathway alterations, and clinical outcomes (2021) · cites this paper as [25]
In the citing paper
“Frequently co-altered genes include TP53, STK11, KEAP1, and CDKN2A.”
From Selective KRAS G12C inhibitors in non-small cell lung cancer: chemistry, concurrent pathway alterations, and clinical outcomes (2021) · cites this paper as [25]
In the citing paper
“Within the KRAS mutant subgroup, lower RNA expression of PTK2 (FAK coding gene) correlates with better survival outcomes”
From Focal Adhesion Kinase (FAK) Inhibition Synergizes with KRAS G12C Inhibitors in Treating Cancer through the Regulation of the FAK–YAP Signaling (2021) · cites this paper as [19]
In the citing paper
“while for KRAS wild type subgroup, there is no difference between the PTK2 low and high expression groups (Figure 1A,B)”
From Focal Adhesion Kinase (FAK) Inhibition Synergizes with KRAS G12C Inhibitors in Treating Cancer through the Regulation of the FAK–YAP Signaling (2021) · cites this paper as [19]
In the citing paper
“Analysis of the data in The Cancer Genome Atlas provides further evidence that a certain fraction of multiple cancers have overexpressed MDMX (amplification or mRNA) concurrently with inactivated (mutated or deleted) p53 (Table 1;34,35).”
From Mdmx promotes genomic instability independent of p53 and Mdm2 (2015) · cites this paper as [34]
In the citing paper
“For example, we evaluated ARF and TP53 status in the data from The Cancer Genome Atlas (TCGA) and determined that malignancies such as squamous cell carcinoma of the lung or head and neck co-inactivate ARF and TP53 in approximately 20% of these tumors (Table 1; (Cerami, et al., 2012; Gao, et al., 2013).”
From The Mdm network and its regulation of p53 activities: a rheostat of cancer risk (2014) · cites this paper as Cerami, et al., 2012
In the citing paper
“However, 5.3% (40 of 760) of breast adenocarcinomas contained amplified USP7 and of those, 75% maintained wild-type TP53 allele status, which implies that USP7 may have other functions related to oncogenesis.”
From The Mdm network and its regulation of p53 activities: a rheostat of cancer risk (2014) · cites this paper as Cerami, et al., 2012
In the citing paper
“Our evaluation of TCGA data revealed that USP7 is rarely amplified in human cancer (Cerami, et al., 2012; Gao, et al., 2013).”
From The Mdm network and its regulation of p53 activities: a rheostat of cancer risk (2014) · cites this paper as Cerami, et al., 2012
In the citing paper
“0.84% (18 of 2148) tumors analyzed had p21 deletions or mutations (Cerami, et al., 2012; Gao, et al., 2013).”
From The Mdm network and its regulation of p53 activities: a rheostat of cancer risk (2014) · cites this paper as Cerami, et al., 2012
In the citing paper
“Our analysis of TCGA data showed that up to 6% of specific human malignancies have amplified MDM2 or MDM4 (and even more have increased MDM2 or MDM4 mRNA expression) with concomitant TP53 mutations”
From The Mdm network and its regulation of p53 activities: a rheostat of cancer risk (2014) · cites this paper as Cerami, et al., 2012
In the citing paper
“even more have increased MDM2 or MDM4 mRNA expression”
From The Mdm network and its regulation of p53 activities: a rheostat of cancer risk (2014) · cites this paper as Cerami, et al., 2012
In the citing paper
“First, Cellosaurus and cBioPortal do not provide cell model functional information, while PharmacoDB does not contain genomic annotation of the cell models and has limited sample/model information.”
From Cell Model Passports-a hub for clinical, genetic and functional datasets of preclinical cancer models (2019) · cites this paper as [36]
In the citing paper
“Third, neither cBioPortal, PharmacoDB nor COSMIC curate samples to map unique identifiers or link samples and models from the same patient, which can be important for identifying mis-identified or cross-contaminated samples.”
From Cell Model Passports-a hub for clinical, genetic and functional datasets of preclinical cancer models (2019) · cites this paper as [36]
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“KRAS is the most frequently mutated oncogene (Cerami et al., 2012; Forbes et al., 2017).”
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“KRAS mutations are implicated in 25–30% of all human cancers, about 19% of non-small cell lung cancers (NSCLCs), about 40% of colorectal cancers (CRCs), and about 73% of pancreatic ductal adenocarcinoma (PDAC) cases (Figure 1) [1,2].”
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“It is an important tumour suppressor gene mutated in 6% of colorectal cancers (CRCs), and germline variants in PTEN are causative of PTEN hamartoma tumour syndrome (Hobert and Eng, 2009; Cerami et al., 2012).”
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Metadata
- Authors
- Cerami, E., Gao, J., Dogrusoz, U., Gross, B. E., Sumer, S. O., Aksoy, B. A., Jacobsen, A., Byrne, C. J., Heuer, M. L., Larsson, E., Antipin, Y., Reva, B., Goldberg, A. P., Sander, C., & Schultz, N.
- Affiliations
- Memorial Sloan Kettering Cancer Center (US)
- Authors' Affiliations: 1Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 2Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York; and 3Computer Engineering Department, Bilkent University, Ankara, Turkey
- Corresponding author
- Cerami, Ethan
- ORCID
- Venue
- Cancer Discovery
- Published
- 2012-05-01
- Volume
- 2
- Issue
- 5
- Pages
- 401-404
- ISSN
- 2159-8274 (ISSN-L)
- 2159-8290
- PMC
- PMC3956037
- OpenAlex
- W2149441684
- Semantic Scholar
- b8d2639696825d163188eb5cea5582c350987b70
- Cited by
- 17,455
- References
- 17
- Citations by year
- 2026: 945 · 2025: 1525 · 2024: 1764 · 2023: 2020 · 2022: 2020 · 2021: 2136 · 2020: 1836 · 2019: 1393 · 2018: 1048 · 2017: 906 · 2016: 764 · 2015: 583 · 2014: 324 · 2013: 159 · 2012: 15
- FWCI
- 114.79
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Cancer Discovery (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Bilkent University Institutional Repository (Bilkent University) (submittedVersion, other-oa)
- Bilkent University Institutional Repository (Bilkent University) (submittedVersion)
- Funders
- Memorial Sloan-Kettering Cancer Center
- University of Toronto
- Bilkent Üniversitesi
- National Institutes of Health
- University of Texas MD Anderson Cancer Center
- Stand Up To Cancer (SU2C‐AACR‐DT0209)
- National Cancer Institute (SU2C-AACR-DT0209, R01CA132744, U24CA143840, NCI-U24CA143840, NCI-R21CA135870, R21CA135870)
- National Institute of General Medical Sciences (GM 103504, P41GM103504)
- National Center for Research Resources (RR031228, P41RR031228)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- cancer genomics data, interactive data exploration, tumor molecular profiles, clinical features, cancer research resources
- MeSH terms
- Database Management Systems, Humans, Neoplasms, Databases, Factual, Internet, Genomics
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