Table_5_VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data.xlsx

Host responses to vaccines are complex but important to investigate. To facilitate the study, we have developed a tool called Vaccine Induced Gene Expression Analysis Tool (VIGET), with the aim to provide an interactive online tool for users to efficiently and robustly analyze the host immune response gene expression data collected in the ImmPort/GEO databases. VIGET allows users to select vaccines, choose ImmPort studies, set up analysis models by choosing confounding variables and two groups of samples having different vaccination times, and then perform differential expression analysis to select genes for pathway enrichment analysis and functional interaction network construction using the Reactome’s web services. VIGET provides features for users to compare results from two analyses, facilitating comparative response analysis across different demographic groups. VIGET uses the Vaccine Ontology (VO) to classify various types of vaccines such as live or inactivated flu vaccines, yellow fever vaccines, etc. To showcase the utilities of VIGET, we conducted a longitudinal analysis of immune responses to yellow fever vaccines and found an intriguing complex activity response pattern of pathways in the immune system annotated in Reactome, demonstrating that VIGET is a valuable web portal that supports effective vaccine response studies using Reactome pathways and ImmPort data.

疫苗诱导的宿主应答机制复杂而重要，有必要进行深入研究。为便于研究，我们开发了一款名为疫苗诱导基因表达分析工具（VIGET）的软件，旨在为用户提供一个交互式的在线平台，以高效且稳健地分析ImmPort/GEO数据库中收集的宿主免疫反应基因表达数据。VIGET允许用户选择疫苗、挑选ImmPort研究项目、通过选择混杂变量以及两组在不同疫苗接种时间点的样本，搭建分析模型，并执行差异表达分析，以选择用于通路富集分析和功能相互作用网络构建的基因。VIGET提供用户比较两次分析结果的功能，便于跨不同人群进行响应分析的对比研究。VIGET采用疫苗本体（VO）对各种类型的疫苗进行分类，例如活疫苗或灭活疫苗、黄热病疫苗等。为展示VIGET的应用价值，我们对黄热病疫苗的免疫反应进行了纵向分析，并发现Reactome中注释的免疫系统中通路呈现出一种引人入胜的复杂活性反应模式，这证明了VIGET是一个支持利用Reactome通路和ImmPort数据进行有效疫苗反应研究的宝贵网络门户。