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

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.

Figure 1.

PaintOmics 3 workflow diagram. PaintOmics 3 takes as input tab delimited files containing processed data from different omic types. After mapping to KEGG database and resolving metabolite ambiguities, a global analysis interface allows filtering, network and enrichment analysis of pathways. Selected pathways can be further analyzed in pathway maps displaying omic data trends and feature-level heatmaps of multi-omic measurements.

Figure 2.

The interactive pathway network in PaintOmics 3. The interactive network panel (A) is complemented by a secondary panel showing the trends for all pathway clusters in a given omic (B), or the trends for each omic in the chosen pathway (C).

Figure 3.

Workspace for pathway exploration in PaintOmics 3. The layout for pathway exploration is divided into three panels. The main panel (A) contains the interactive pathway diagram, the Global Heatmap panel (B) displays multi-omics data in the form of heatmaps, and the Pathway Information panel (C) contains search and summarizing functions.

Figure 4.

Part of the results for the PaintOmics pathway enrichment analysis for Cacchiarelli’s data (complete list in Supplementary Figure S5). The enriched pathways are ordered by the combined P-value. Upper positions correspond to the most significant pathways. A color scale is used to highlight the level of enrichment for each pathway where the higher the intensity of red, the higher the significance. Gray cells indicate that the corresponding omic data type is not present in the pathway.

Figure 5.

Pathway networks and cluster profiles of representative temporal patterns. Network A is colored according to gene expression data. Network B is colored according to H3K4me3 ChIP-seq data.

Figure 6.

Interactive KEGG diagram for Signaling pathways regulating pluripotency of stem cells. Data obtained from Cacchiarelli’s multi-omics study