PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data

TLDR

The growing availability of multi‑omic platforms creates new analytical challenges, and joint visualization of these data is essential for uncovering cross‑layer interactions and maximizing biological insight. PaintOmics 3 is a web‑based resource that integrates multiple omic data types onto KEGG pathway diagrams for interactive exploration. It combines server‑side analysis with modern web visualization, providing automatic identifier conversion, multi‑layer matching, pathway enrichment, network analysis, heatmaps, trend charts, and supports transcriptomics, proteomics, metabolomics, ATAC‑seq, ChIP‑seq, and is freely available at www.paintomics.org.

Abstract

The increasing availability of multi-omic platforms poses new challenges to data analysis. Joint visualization of multi-omics data is instrumental in better understanding interconnections across molecular layers and in fully utilizing the multi-omic resources available to make biological discoveries. We present here PaintOmics 3, a web-based resource for the integrated visualization of multiple omic data types onto KEGG pathway diagrams. PaintOmics 3 combines server-end capabilities for data analysis with the potential of modern web resources for data visualization, providing researchers with a powerful framework for interactive exploration of their multi-omics information. Unlike other visualization tools, PaintOmics 3 covers a comprehensive pathway analysis workflow, including automatic feature name/identifier conversion, multi-layered feature matching, pathway enrichment, network analysis, interactive heatmaps, trend charts, and more. It accepts a wide variety of omic types, including transcriptomics, proteomics and metabolomics, as well as region-based approaches such as ATAC-seq or ChIP-seq data. The tool is freely available at www.paintomics.org