Multiomics2Targets identifies targets from cancer cohorts profiled with transcriptomics, proteomics, and phosphoproteomics.

IF 4.3 Q1 BIOCHEMICAL RESEARCH METHODS Cell Reports Methods Pub Date : 2024-08-19 Epub Date: 2024-08-09 DOI:10.1016/j.crmeth.2024.100839

Eden Z Deng, Giacomo B Marino, Daniel J B Clarke, Ido Diamant, Adam C Resnick, Weiping Ma, Pei Wang, Avi Ma'ayan

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Abstract

The availability of data from profiling of cancer patients with multiomics is rapidly increasing. However, integrative analysis of such data for personalized target identification is not trivial. Multiomics2Targets is a platform that enables users to upload transcriptomics, proteomics, and phosphoproteomics data matrices collected from the same cohort of cancer patients. After uploading the data, Multiomics2Targets produces a report that resembles a research publication. The uploaded matrices are processed, analyzed, and visualized using the tools Enrichr, KEA3, ChEA3, Expression2Kinases, and TargetRanger to identify and prioritize proteins, genes, and transcripts as potential targets. Figures and tables, as well as descriptions of the methods and results, are automatically generated. Reports include an abstract, introduction, methods, results, discussion, conclusions, and references and are exportable as citable PDFs and Jupyter Notebooks. Multiomics2Targets is applied to analyze version 3 of the Clinical Proteomic Tumor Analysis Consortium (CPTAC3) pan-cancer cohort, identifying potential targets for each CPTAC3 cancer subtype. Multiomics2Targets is available from https://multiomics2targets.maayanlab.cloud/.

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Multiomics2Targets 可从使用转录组学、蛋白质组学和磷酸蛋白组学分析的癌症队列中识别靶点。

利用多组学技术对癌症患者进行分析所获得的数据正在迅速增加。然而，综合分析这些数据以进行个性化靶点鉴定并非易事。Multiomics2Targets 是一个平台，用户可以上传从同一癌症患者队列中收集的转录组学、蛋白质组学和磷酸化蛋白质组学数据矩阵。上传数据后，Multiomics2Targets 会生成一份类似研究出版物的报告。使用 Enrichr、KEA3、ChEA3、Expression2Kinases 和 TargetRanger 等工具对上传的矩阵进行处理、分析和可视化，以确定蛋白质、基因和转录本作为潜在靶点的优先级。图和表以及方法和结果的描述都是自动生成的。报告包括摘要、介绍、方法、结果、讨论、结论和参考文献，并可导出为可引用的 PDF 文件和 Jupyter 笔记本。Multiomics2Targets应用于分析临床肿瘤蛋白质组学分析联盟（CPTAC3）泛癌症队列的第3版，为每个CPTAC3癌症亚型确定潜在靶点。Multiomics2Targets 可从 https://multiomics2targets.maayanlab.cloud/ 获取。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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