Abstract

Protein–protein interactions (PPIs) are crucial to mediate biological functions, and understanding PPIs in cancer type-specific context could help decipher the underlying molecular mechanisms of tumorigenesis and identify potential therapeutic options. Therefore, we update the Protein Interaction Network Analysis (PINA) platform to version 3.0, to integrate the unified human interactome with RNA-seq transcriptomes and mass spectrometry-based proteomes across tens of cancer types. A number of new analytical utilities were developed to help characterize the cancer context for a PPI network, which includes inferring proteins with expression specificity and identifying candidate prognosis biomarkers, putative cancer drivers, and therapeutic targets for a specific cancer type; as well as identifying pairs of co-expressing interacting proteins across cancer types. Furthermore, a brand-new web interface has been designed to integrate these new utilities within an interactive network visualization environment, which allows users to quickly and comprehensively investigate the roles of human interacting proteins in a cancer type-specific context. PINA is freely available at https://omics.bjcancer.org/pina/.

中文翻译：

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PINA 3.0：挖掘癌症相互作用组

摘要

蛋白质间相互作用（PPI）对于介导生物学功能至关重要，了解癌症特定类型背景下的PPI可能有助于破译肿瘤发生的潜在分子机制并确定潜在的治疗选择。因此，我们将蛋白质相互作用网络分析（PINA）平台更新为3.0版，以将统一的人类相互作用基因组与跨越数十种癌症类型的RNA-seq转录组和基于质谱的蛋白质组进行整合。开发了许多新的分析工具来帮助表征PPI网络的癌症背景，包括推断具有表达特异性的蛋白质并鉴定候选预后生物标志物，推定的癌症驱动器和特定癌症类型的治疗靶点；以及识别跨癌症类型的共表达相互作用蛋白对。此外，还设计了一个全新的Web界面，以将这些新实用程序集成到交互式网络可视化环境中，从而使用户可以快速，全面地研究人类相互作用蛋白在特定于癌症类型的情况下的作用。可从https://omics.bjcancer.org/pina/免费获得PINA。