研究动态
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IMOPAC: 一个用于患者衍生癌细胞系的互动性多组学和药理学分析的网络服务器。

IMOPAC: A web server for interactive multiomics and pharmacological analyses of patient-derived cancer cell lines.

发表日期:2023
作者: Ganxun Li, Dongyi Wan, Junnan Liang, Peng Zhu, Zeyang Ding, Bixiang Zhang
来源: Epigenetics & Chromatin

摘要:

多个大型合作项目,包括NCI-60、GDSC和DepMap已经建立了大规模的多维肿瘤基因组和药理学分析数据,为数据挖掘和进一步了解内在治疗反应机制提供了新的机会。然而,对于实验生物学家,尤其是没有生物信息学背景的人来说,整合、探索和分析这些庞大的药物基因组数据愈加具有挑战性。为了弥补这一空白,我们引入了一个交互式、易于使用的基于网络的工具IMOPAC,它提供了基于这三个公共数据库的快速可视化和可定制功能,能够将细胞系的药物基因组数据转化为易于理解的遗传、表观遗传、转录、蛋白质、代谢和药理学事件。用户友好的查询界面以及定制化的数据存储使得用户能够互动地研究和可视化基因和通路中的多组学变化,并将这些变化与不同癌症类型的细胞系中的药物反应联系起来。我们门户网站中的分析包括全癌症表达、药物-组学/通路相关性、癌症亚型、组学-组学(顺着/反着调节)相关性、融合查询分析和药物反应预测分析。通过简单点击IMOPAC进行的全面多组学和药物基因组分析将显著地有益于肿瘤精准医学,有助于发现潜在的生物学机制,并促进了临床行动性生物标志物的药物基因组挖掘,从而不仅对基础研究人员,而且对临床从业者都具有重要意义。IMOPAC可以免费访问http://www.hbpding.com/IMOPAC.©2023 Research Network of Computational and Structural Biotechnology, Elsevier B.V.出版。
Large-scale multidimensional cancer genomic and pharmacological profiles have been created by several large consortium projects, including NCI-60, GDSC and DepMap, providing novel opportunities for data mining and further understanding of intrinsic therapeutic response mechanisms. However, it is increasingly challenging for experimental biologists, especially those without a bioinformatic background, to integrate, explore, and analyse these tremendous pharmacogenomics. To address this gap, IMOPAC, an interactive and easy-to-use web-based tool, was introduced to provide rapid visualizations and customizable functionalities on the basis of these three publicly available databases, which may reduce pharmacogenomic profiles from cell lines into readily understandable genetic, epigenetic, transcriptionomic, proteomic, metabolomic, and pharmacological events. The user-friendly query interface together with customized data storage enables users to interactively investigate and visualize multiomics alterations across genes and pathways and to link these alterations with drug responses across cell lines from diverse cancer types. The analyses in our portal include pancancer expression, drug-omics/pathway correlation, cancer subtypes, omics-omics (cis-/trans-regulation) correlation, fusion query analysis, and drug response prediction analysis. The comprehensive multiomics and pharmacogenomic analyses with simple clicking through IMOPAC will significantly benefit cancer precision medicine, contribute to the discoveries of potential biological mechanisms and facilitate pharmacogenomics mining in the identification of clinically actionable biomarkers for both basic researchers and clinical practitioners. IMOPAC is freely available at http://www.hbpding.com/IMOPAC.© 2023 Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.