Yue Zongliang, Slominski Radomir, Bharti Samuel, Chen Jake Y
Informatics Institute in the School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States.
Graduate Biomedical Sciences Program, The University of Alabama at Birmingham, Birmingham, AL, United States.
Front Genet. 2022 Apr 12;13:820361. doi: 10.3389/fgene.2022.820361. eCollection 2022.
Functional genomics studies have helped researchers annotate differentially expressed gene lists, extract gene expression signatures, and identify biological pathways from omics profiling experiments conducted on biological samples. The current geneset, network, and pathway analysis (GNPA) web servers, e.g., DAVID, EnrichR, WebGestaltR, or PAGER, do not allow automated integrative functional genomic downstream analysis. In this study, we developed a new web-based interactive application, "PAGER Web APP", which supports online R scripting of integrative GNPA. In a case study of melanoma drug resistance, we showed that the new PAGER Web APP enabled us to discover highly relevant pathways and network modules, leading to novel biological insights. We also compared PAGER Web APP's pathway analysis results retrieved among PAGER, EnrichR, and WebGestaltR to show its advantages in integrative GNPA. The interactive online web APP is publicly accessible from the link, https://aimed-lab.shinyapps.io/PAGERwebapp/.
功能基因组学研究帮助研究人员注释差异表达基因列表、提取基因表达特征，并从对生物样本进行的组学分析实验中识别生物途径。当前的基因集、网络和途径分析（GNPA）网络服务器，如DAVID、EnrichR、WebGestaltR或PAGER，不允许进行自动化的综合功能基因组下游分析。在本研究中，我们开发了一个新的基于网络的交互式应用程序“PAGER网络应用程序”，它支持综合GNPA的在线R脚本编写。在一项黑色素瘤耐药性的案例研究中，我们表明新的PAGER网络应用程序使我们能够发现高度相关的途径和网络模块，从而获得新的生物学见解。我们还比较了在PAGER、EnrichR和WebGestaltR中检索到的PAGER网络应用程序的途径分析结果，以展示其在综合GNPA中的优势。这个交互式在线网络应用程序可通过链接https://aimed-lab.shinyapps.io/PAGERwebapp/公开访问。
