ProFun: A web server for functional enrichment analysis of parasitic protozoan genes

Po-Jung Huang; Yi-Chen Weng; Kuo-Yang Huang; Chi-Ching Lee; Yuan-Ming Yeh; Yu-Tong Chen; Cheng-Hsun Chiu; Petrus Tang

doi:10.1016/j.jmii.2024.01.007

ProFun: A web server for functional enrichment analysis of parasitic protozoan genes

J Microbiol Immunol Infect. 2024 Feb 1:S1684-1182(24)00008-2. doi: 10.1016/j.jmii.2024.01.007. Online ahead of print.

Authors

Po-Jung Huang¹, Yi-Chen Weng², Kuo-Yang Huang³, Chi-Ching Lee⁴, Yuan-Ming Yeh⁵, Yu-Tong Chen⁶, Cheng-Hsun Chiu⁷, Petrus Tang⁸

Affiliations

¹ Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan; Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan. Electronic address: pjhuang@gap.cgu.edu.tw.
² School of Medicine, Chang Gung University, Taoyuan, Taiwan. Electronic address: yichenweng91@gmail.com.
³ Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei, Taiwan. Electronic address: cguhgy6934@gmail.com.
⁴ Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan; Department and Graduate Institute of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan. Electronic address: chichinglee@cgu.edu.tw.
⁵ Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan. Electronic address: ymyeh@cgmh.org.tw.
⁶ Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan. Electronic address: linda417619@gmail.com.
⁷ Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan. Electronic address: chchiu@cgmh.org.tw.
⁸ Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan; Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan, Taiwan. Electronic address: petang@mail.cgu.edu.tw.

PMID: 38311498
DOI: 10.1016/j.jmii.2024.01.007

Abstract

Background: The initial step to interpreting putative biological functions from comparative multi-omics studies usually starts from a differential expressed gene list followed by functional enrichment analysis (FEA). However, most FEA packages are designed exclusively for humans and model organisms. Although parasitic protozoan is the most important pathogen in the tropics, no FEA package is available for protozoan functional (ProFun) enrichment analysis. To speed up comparative multi-omics research on parasitic protozoans, we constructed ProFun, a web-based, user-friendly platform for the research community.

Methods: ProFun utilizes the Docker container, ShinyProxy, and R Shiny to construct a scalable web service with load-balancing infrastructure. We have integrated a series of visual analytic functions, in-house scripts, and custom-made annotation packages to create three analytical modules for 40 protozoan species: (1) Gene Overlaps; (2) Over-representation Analysis (ORA); (3) Gene Set Enrichment Analysis (GSEA).

Results: We have established ProFun, a web server for functional enrichment analysis of differentially expressed genes. FEA becomes as simple as pasting a list of gene IDs into the textbox of our website. Users can customize enrichment parameters and results with just one click. The intuitive web interface and publication-ready charts enable users to reveal meaningful biological events and pinpoint potential targets for further studies.

Conclusion: ProFun is the first web application that enables gene functional enrichment analysis of parasitic protozoans. In addition to supporting FEA analysis, ProFun also allows the comparison of FEA results across complicated experimental designs. ProFun is freely available at http://dalek.cgu.edu.tw:8080/app/profun.

Keywords: Gene functional enrichment; Protozoan; Transcriptome; Web server.