‡Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016; §Institute for Systems Genetics, New York University School of Medicine, New York, NY 10016; ¶Sackler Institute of Graduate Biomedical Sciences, New York University School of Medicine, New York, NY 10016.
‖Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065.
Mol Cell Proteomics. 2019 Sep;18(9):1893-1898. doi: 10.1074/mcp.TIR119.001673. Epub 2019 Jul 15.
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.
临床蛋白质组肿瘤分析联盟（CPTAC）已经为癌症基因组图谱（TCGA）中的选定的乳腺癌、结肠癌和卵巢肿瘤生成了广泛的基于质谱的蛋白质组学数据。我们已经将 CPTAC 蛋白质组学数据纳入 cBioPortal 中，以支持在同一肿瘤的临床和基因组数据背景下轻松探索和整合分析这些蛋白质组数据集。cBioPortal 是一个用于探索、可视化和分析多维癌症基因组学和临床数据的开源平台。cBioPortal 的公共实例（http://cbioportal.org/）托管了 200 多个癌症基因组学研究，包括 TCGA 的所有数据。它的生物学家友好的界面提供了许多丰富的分析功能，包括多个平台上基因水平数据的图形摘要、基因或其他数据类型之间的相关性分析、生存分析以及每个患者数据的可视化。在这里，我们介绍了将 CPTAC 基于质谱的蛋白质组学数据集成到 cBioPortal 中的情况，其中包括已经由 TCGA 进行突变、拷贝数改变、基因表达和 DNA 甲基化分析的 77 例乳腺癌、95 例结直肠癌和 174 例卵巢肿瘤。结果，现在可以在 cBioPortal 中轻松地在临床和基因组学数据的背景下探索和分析 CPTAC 数据。通过将 CPTAC 数据集成到 cBioPortal 中，可以克服 TCGA 蛋白质组阵列数据的局限性，同时还提供了用户友好的 Web 界面、Web API 和 R 客户端，以便与基因组、表观基因组和临床数据一起查询质谱数据。
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