PAGER Web APP: An Interactive, Online Gene Set and Network Interpretation Tool for Functional Genomics

Zongliang Yue; Radomir Slominski; Samuel Bharti; Jake Y Chen

doi:10.3389/fgene.2022.820361

PAGER Web APP: An Interactive, Online Gene Set and Network Interpretation Tool for Functional Genomics

Front Genet. 2022 Apr 12:13:820361. doi: 10.3389/fgene.2022.820361. eCollection 2022.

Authors

Zongliang Yue¹, Radomir Slominski^{1

2}, Samuel Bharti¹, Jake Y Chen¹

Affiliations

¹ Informatics Institute in the School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States.
² Graduate Biomedical Sciences Program, The University of Alabama at Birmingham, Birmingham, AL, United States.

Abstract

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/.

Keywords: GNPA; PAGER; PAGER Web APP; functional genomics; geneset analysis; melanoma; network visualization and analysis.