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Connecting omics signatures and revealing biological mechanisms with iLINCS
Nature Communications ( IF 14.7 ) Pub Date : 2022-08-09 , DOI: 10.1038/s41467-022-32205-3
Marcin Pilarczyk 1, 2, 3, 4 , Mehdi Fazel-Najafabadi 1, 2, 3, 4 , Michal Kouril 2, 3, 4, 5 , Behrouz Shamsaei 1, 2, 3, 4 , Juozas Vasiliauskas 1, 2, 3, 4 , Wen Niu 1, 2, 3, 4 , Naim Mahi 1, 2, 3, 4 , Lixia Zhang 1, 2, 3, 4 , Nicholas A Clark 1, 2, 3, 4 , Yan Ren 1, 2, 3, 4 , Shana White 1, 2, 3, 4 , Rashid Karim 1, 6 , Huan Xu 1, 2, 3, 4 , Jacek Biesiada 1 , Mark F Bennett 1, 2, 3, 4 , Sarah E Davidson 1 , John F Reichard 1, 2, 3, 4 , Kurt Roberts 1 , Vasileios Stathias 2, 3, 4, 7 , Amar Koleti 2, 3, 4, 7 , Dusica Vidovic 2, 3, 4, 7 , Daniel J B Clarke 2, 3, 4, 8 , Stephan C Schürer 2, 3, 4, 7 , Avi Ma'ayan 2, 3, 4, 8 , Jarek Meller 1, 2, 3, 4, 5, 6 , Mario Medvedovic 1, 2, 3, 4
Affiliation  

There are only a few platforms that integrate multiple omics data types, bioinformatics tools, and interfaces for integrative analyses and visualization that do not require programming skills. Here we present iLINCS (http://ilincs.org), an integrative web-based platform for analysis of omics data and signatures of cellular perturbations. The platform facilitates mining and re-analysis of the large collection of omics datasets (>34,000), pre-computed signatures (>200,000), and their connections, as well as the analysis of user-submitted omics signatures of diseases and cellular perturbations. iLINCS analysis workflows integrate vast omics data resources and a range of analytics and interactive visualization tools into a comprehensive platform for analysis of omics signatures. iLINCS user-friendly interfaces enable execution of sophisticated analyses of omics signatures, mechanism of action analysis, and signature-driven drug repositioning. We illustrate the utility of iLINCS with three use cases involving analysis of cancer proteogenomic signatures, COVID 19 transcriptomic signatures and mTOR signaling.



中文翻译:


使用 iLINCS 连接组学特征并揭示生物学机制



只有少数平台集成了多种组学数据类型、生物信息学工具以及不需要编程技能的综合分析和可视化界面。在这里,我们介绍 iLINCS (http://ilincs.org),这是一个基于网络的综合平台,用于分析组学数据和细胞扰动的特征。该平台有助于挖掘和重新分析大量组学数据集 (>34,000)、预先计算的特征 (>200,000) 及其连接,以及分析用户提交的疾病组学特征和细胞扰动。 iLINCS 分析工作流程将大量组学数据资源以及一系列分析和交互式可视化工具集成到一个用于分析组学特征的综合平台中。 iLINCS 用户友好的界面可以执行复杂的组学特征分析、作用机制分析和特征驱动的药物重新定位。我们通过三个用例说明了 iLINCS 的实用性,涉及癌症蛋白质组特征、COVID 19 转录组特征和 mTOR 信号转导分析。

更新日期:2022-08-10
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