ArticleMolecular & cellular proteomics : MCP2019
Integration and Analysis of CPTAC Proteomics Data in the Context of Cancer Genomics in the cBioPortal.
Article in Molecular & cellular proteomics : MCP, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 114 papers, 1 of them a synthesis that pooled it.
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Who cites it
114 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Pan-cancer analysis reveals FOLH1 as a prognostic biomarker and immune modulator in human tumors.Translational cancer research · 2026Article
- GCN2 in Cancer: Molecular Mechanisms to Therapeutic Potential.Current cancer drug targets · 2026Review
- Association of MTUS1 with cisplatin response in head and neck squamous cell carcinoma: a retrospective cohort analysis of The Cancer Genome Atlas data.Journal of Yeungnam medical science · 2026Article
- Analytical Techniques as Indicators of Biomarkers in Proteomics Cancer Diagnosis.Anti-cancer agents in medicinal chemistry · 2026Review
- Comprehensive pan-cancer analysis of KRT6A as a prognostic and immune biomarker.Scientific reports · 2025Article
- Association of HTR1F with Prognosis, Tumor Immune Microenvironment, and Drug Sensitivity in Cancer: A Multi-Omics Perspective.Biomedicines · 2025Article
- UPP1 and AHSA1 as emerging biomarkers and targets in pancreatic cancer: A proteomic approach.Biomolecules & biomedicine · 2025Article
- Key genes altered in glioblastoma based on bioinformatics (Review).Oncology letters · 2025Review
- Rapid assay development for low input targeted proteomics using a versatile linear ion trap.Nature communications · 2025Article
- Comprehensive analysis of mRNA expression of Piezo1 and Piezo2 in tumor samples and their prognostic implications in gastric cancer.Discover oncology · 2025Article
- Integrative Analysis of DNA Methylation and microRNA Reveals GNPDA1 and SLC25A16 Related to Biopsychosocial Factors Among Taiwanese Women with a Family History of Breast Cancer.Journal of personalized medicine · 2025Article
- Proteogenomic discovery ofScience advances · 2025Article
- Empowering personalized oncology: evolution of digital support and visualization tools for molecular tumor boards.BMC medical informatics and decision making · 2025Article
- Deciphering the let-7c-5p/RRM2 axis in lung adenocarcinoma: expression, prognosis, and immune landscape implications.Frontiers in oncology · 2025Article
- Exploring the role of LOX family in glioma progression and immune modulation.Frontiers in immunology · 2025Article
- Increased SLC7A3 Expression Inhibits Tumor Cell Proliferation and Predicts a Favorable Prognosis in Breast Cancer.Recent patents on anti-cancer drug discovery · 2025Article
54 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
Abstract
The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has produced extensive mass spectrometry-based proteomics data for selected breast, colon, and ovarian tumors from The Cancer Genome Atlas (TCGA). We have incorporated the CPTAC proteomics data into the cBioPortal to support easy exploration and integrative analysis of these proteomic datasets in the context of the clinical and genomics data from the same tumors. cBioPortal is an open source platform for exploring, visualizing, and analyzing multidimensional cancer genomics and clinical data. The public instance of the cBioPortal (http://cbioportal.org/) hosts more than 200 cancer genomics studies, including all of the data from TCGA. Its biologist-friendly interface provides many rich analysis features, including a graphical summary of gene-level data across multiple platforms, correlation analysis between genes or other data types, survival analysis, and per-patient data visualization. Here, we present the integration of the CPTAC mass spectrometry-based proteomics data into the cBioPortal, consisting of 77 breast, 95 colorectal, and 174 ovarian tumors that already have been profiled by TCGA for mutations, copy number alterations, gene expression, and DNA methylation. As a result, the CPTAC data can now be easily explored and analyzed in the cBioPortal in the context of clinical and genomics data. By integrating CPTAC data into cBioPortal, limitations of TCGA proteomics array data can be overcome while also providing a user-friendly web interface, a web API, and an R client to query the mass spectrometry data together with genomic, epigenomic, and clinical data.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.