Shiny AMMOA: an interactive platform for integrative multi-omics analysis of murine aging

Aging is accompanied by complex, tissue-specific molecular changes across multiple biological layers, yet integrative analysis of multi-omics datasets remains challenging for many experimental researchers due to technical and computational barriers. Here, I present Shiny Aging Murine Multi-Omic Analyzer (Shiny AMMOA), a graphical user interface (GUI)-based, user-friendly analytical platform that enables interactive exploration of murine aging-associated bulk transcriptomic, proteomic, and metabolomic datasets. Shiny AMMOA integrates publicly available multi-omics resources within a unified R Shiny framework and supports end-to-end analyses, including differential expression testing, pathway enrichment analysis, and pathway-level visualization across individual and multiple omics layers. Using representative use cases, I demonstrate that Shiny AMMOA recapitulates key findings from original source studies and facilitates intuitive discovery of tissue-, pathway-, and modality-specific aging signatures, including age-associated alterations in unfolded protein response, extracellular matrix organization, and metabolic pathways across specific tissues and omics layers. The platform further enables integrated visualization of molecular changes across omics layers on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway diagrams, supporting hypothesis generation at the systems level. By democratizing access to integrative multi-omics analysis while preserving analytical rigor, Shiny AMMOA provides an extensible resource for experimental biologists and aging researchers to interrogate large-scale public datasets, prioritize biological pathways, and accelerate translation of multi-omics insights into testable experimental hypotheses. Shiny AMMOA is available at https://github.com/M-Ninomiya-Kanda/Shiny_AMMOA_local, and a lightweight web-based demonstration version with limited functionality is available at https://m-ninomiya-kanda.shinyapps.io/shiny_ammoa_web/.