To better understand the molecular basis of cancer, the NCI's Clinical Proteomics Tumor Analysis Consortium (CPTAC) has been performing comprehensive large‐scale proteogenomic characterizations of multiple cancer types. Gene and protein regulatory networks are subsequently being derived based on these proteogenomic profiles, which serve as tools to gain systems‐level understanding of the molecular regulatory factories underlying these diseases. On the other hand, it remains a challenge to effectively visualize and navigate the resulting network models, which capture higher order structures in the proteogenomic profiles. There is a pressing need to have a new open community resource tool for intuitive visual exploration, interpretation, and communication of these gene/protein regulatory networks by the cancer research community. In this work, ProNetView‐ccRCC (http://ccrcc.cptac-network-view.org/), an interactive web‐based network exploration portal for investigating phosphopeptide co‐expression network inferred based on the CPTAC clear cell renal cell carcinoma (ccRCC) phosphoproteomics data is introduced. ProNetView‐ccRCC enables quick, user‐intuitive visual interactions with the ccRCC tumor phosphoprotein co‐expression network comprised of 3614 genes, as well as 30 functional pathway‐enriched network modules. Users can interact with the network portal and can conveniently query for association between abundance of each phosphopeptide in the network and clinical variables such as tumor grade.

中文翻译：

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ProNetView-ccRCC：交互式探索透明细胞肾细胞癌蛋白质基因组网络的基于 Web 的门户。

为了更好地了解癌症的分子基础，NCI 的临床蛋白质组学肿瘤分析联盟 (CPTAC) 一直在对多种癌症类型进行全面的大规模蛋白质基因组表征。随后根据这些蛋白质组图谱衍生出基因和蛋白质调控网络，这些蛋白质组图谱可作为获得对这些疾病背后的分子调控工厂的系统级理解的工具。另一方面，有效地可视化和导航生成的网络模型仍然是一个挑战，这些模型捕获蛋白质组谱中的高阶结构。癌症研究界迫切需要一种新的开放社区资源工具，用于对这些基因/蛋白质调控网络进行直观的视觉探索、解释和交流。在这项工作中，ProNetView-ccRCC (http://ccrcc.cptac-network-view.org/)，一个基于交互式网络的网络探索门户，用于研究基于 CPTAC 透明细胞肾细胞癌推断的磷酸肽共表达网络 ( ccRCC）磷酸蛋白质组学数据被介绍。ProNetView-ccRCC 能够与由 3614 个基因以及 30 个功能通路丰富的网络模块组成的 ccRCC 肿瘤磷蛋白共表达网络进行快速、用户直观的视觉交互。用户可以与网络门户进行交互，并可以方便地查询网络中每种磷酸肽的丰度与肿瘤分级等临床变量之间的关联。