Year: 2025
Type: article
Abstract: Description RNA sequencing (RNA-seq) is a powerful and widely used technique in immunology to extract insights from biological data. However, software tools for inferring cytokine activities based on RNA-seq data have been limited. To address this gap, we created a web application that hosts our Immune Dictionary, a compendium of single-cell transcriptomic profiles of over 17 cell types in response to each of 86 cytokines in mouse lymph nodes in vivo, and its companion software, Immune Response Enrichment Analysis (IREA), that allows assessment of cytokine activities and immune cell polarization from gene expression data. Our web application allows for exploratory visualization of cytokine stimulation response in each major immune cell type and is optimized for browsing perturbational single-cell RNA-sequencing data. Furthermore, researchers can easily enter a list of genes involved in an immune process, and the IREA web portal will provide the predictions of key cytokines driving the immune process within minutes. Recent updates to the web portal include accelerated graph displays, expanded network analysis, additional coverage of immunostimulatory agents such as chemokines, and comprehensive user instructions for each software functionality. The study highlights the power of big data in accelerating advancements in immunology and immunotherapies and provides a freely available software tool for the biomedical research community to investigate cytokine-mediated gene regulation. Funding Sources Harvard School of Dental Medicine start-up funds Topic Categories Computational and Systems Immunology (COMP)
Source: The Journal of Immunology
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: bronze
OpenAlex ID: W4416447387
FWCI:
Cites:
Cited by:
Related to: