Department of Anatomy and Physiology, University of Melbourne, Melbourne, VIC 3010, Australia.
Department of Biological Chemistry and Center for Epigenetics and Metabolism, University of California, Irvine, CA 92697, USA.
Nucleic Acids Res. 2021 Jul 2;49(W1):W104-W113. doi: 10.1093/nar/gkab352.
The integration of genomics, transcriptomics, proteomics and phenotypic traits across genetically diverse populations is a powerful approach to discover novel biological regulators. The increasing volume of complex data require new and easy-to-use tools accessible to a variety of scientists for the discovery and visualization of functionally relevant associations. To meet this requirement, we developed CoffeeProt, an open-source tool that analyses genetic variants associated to protein networks, other omics datatypes and phenotypic traits. CoffeeProt uses transcriptomics or proteomics data to perform correlation network analyses and annotates results with protein-protein interactions, subcellular localisations and drug associations. It then integrates genetic variants associated with gene expression (eQTLs) or protein abundance (pQTLs) and includes predictions of the potential consequences of variants on gene function. Finally, genetic variants are co-mapped to molecular or phenotypic traits either provided by the user or retrieved directly from publicly available GWAS results. We demonstrate its utility with the analysis of mouse and human population data enabling the rapid identification of genetic variants associated with druggable proteins and clinical traits. We expect that CoffeeProt will serve the systems genetics and basic science research communities, leading to the discovery of novel biologically relevant associations. CoffeeProt is available at www.coffeeprot.com.
跨遗传多样性群体整合基因组学、转录组学、蛋白质组学和表型特征是发现新的生物学调节剂的一种强大方法。越来越多的复杂数据需要新的、易于使用的工具，供各种科学家用于发现和可视化功能相关的关联。为了满足这一要求，我们开发了 CoffeeProt，这是一个开源工具，用于分析与蛋白质网络、其他组学数据类型和表型特征相关的遗传变异。CoffeeProt 使用转录组学或蛋白质组学数据来执行相关网络分析，并将结果与蛋白质-蛋白质相互作用、亚细胞定位和药物关联进行注释。然后，它将与基因表达（eQTLs）或蛋白质丰度（pQTLs）相关的遗传变异进行整合，并包括对变异对基因功能潜在影响的预测。最后，将遗传变异与用户提供或直接从公开可用的 GWAS 结果中检索到的分子或表型特征进行共映射。我们通过分析小鼠和人类群体数据来展示其效用，从而能够快速识别与可用药蛋白和临床特征相关的遗传变异。我们预计 CoffeeProt 将服务于系统遗传学和基础科学研究社区，从而发现新的具有生物学相关性的关联。CoffeeProt 可在 www.coffeeprot.com 上获得。
