To allow multi-omics comparison of plasma proteomics, head kidney proteomics, and single-cell RNA sequencing in the kidney marrow, we generated KIAMO (Killifish Immune Aging MultiOmics). KIAMO is a web-based analysis tool designed to explore the effects of aging on gene expression in killifish (GRZ-AD strain) at the proteomics and single-cell RNA sequencing (scRNA-Seq) levels. We designed KIAMO using a user-friendly Shiny interface to facilitate direct visualization and comparison across these datasets within immune organs. The platform offers several key features and benefits for the wider killifish and aging research community:
- Gene Comparison Across Omic Layers: KIAMO provides comparisons across multi-omics data, including plasma proteomics, kidney marrow proteomics, and single-cell RNA sequencing from kidney marrow, enabling researchers to conduct comparative analyses of immune aging in killifish.
- Visualization Tools: The platform provides intuitive visualization tools, such as scRNASeq tSNEs highlighted per gene, heatmaps showing cell type specificity of gene expression, and boxplots for proteomics data, including statistical tests, that show differences between young and old protein levels.
- User-Friendly Interface: The Shiny app interface is designed for ease of use, making it accessible even for researchers with no bioinformatics expertise.
- Community Resource: KIAMO serves as a valuable resource for the wider research community, offering ways to start exploring gene and protein expression patterns, either focusing on certain age-related changes or specific genes across immune organs and cell types.
Use Case Example: For instance, a researcher interested in identifying biomarkers of immune aging can use KIAMO to choose proteins with increased abundance in older plasma and head kidney tissues and to correlate these findings with single-cell RNA sequencing data from the same tissues.
For more detailed information, detailed use cases, and to explore the platform's features, please visit the KIAMO Wiki.
Data exploration tool accompanying Morabito et al. manuscript on ageing of the immune system in killifish.
Shiny app is available via: https://genome.leibniz-fli.de/shiny/kiamo/