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

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 respon...

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Autores principales: Brunson, Timothy, Sanati, Nasim, Huffman, Anthony, Masci, Anna Maria, Zheng, Jie, Cooke, Michael F., Conley, Patrick, He, Yongqun, Wu, Guanming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10172660/
https://www.ncbi.nlm.nih.gov/pubmed/37180100
http://dx.doi.org/10.3389/fimmu.2023.1141030
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author Brunson, Timothy
Sanati, Nasim
Huffman, Anthony
Masci, Anna Maria
Zheng, Jie
Cooke, Michael F.
Conley, Patrick
He, Yongqun
Wu, Guanming
author_facet Brunson, Timothy
Sanati, Nasim
Huffman, Anthony
Masci, Anna Maria
Zheng, Jie
Cooke, Michael F.
Conley, Patrick
He, Yongqun
Wu, Guanming
author_sort Brunson, Timothy
collection PubMed
description 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.
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spelling pubmed-101726602023-05-12 VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data Brunson, Timothy Sanati, Nasim Huffman, Anthony Masci, Anna Maria Zheng, Jie Cooke, Michael F. Conley, Patrick He, Yongqun Wu, Guanming Front Immunol Immunology 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. Frontiers Media S.A. 2023-03-21 /pmc/articles/PMC10172660/ /pubmed/37180100 http://dx.doi.org/10.3389/fimmu.2023.1141030 Text en Copyright © 2023 Brunson, Sanati, Huffman, Masci, Zheng, Cooke, Conley, He and Wu https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Immunology
Brunson, Timothy
Sanati, Nasim
Huffman, Anthony
Masci, Anna Maria
Zheng, Jie
Cooke, Michael F.
Conley, Patrick
He, Yongqun
Wu, Guanming
VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data
title VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data
title_full VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data
title_fullStr VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data
title_full_unstemmed VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data
title_short VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data
title_sort viget: a web portal for study of vaccine-induced host responses based on reactome pathways and immport data
topic Immunology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10172660/
https://www.ncbi.nlm.nih.gov/pubmed/37180100
http://dx.doi.org/10.3389/fimmu.2023.1141030
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