Visualizing set relationships: EVenn's comprehensive approach to Venn diagrams

Abstract

Venn diagrams serve as invaluable tools for visualizing set relationships due to their ease of interpretation. Widely applied across diverse disciplines such as metabolomics, genomics, transcriptomics, and proteomics, their utility is undeniable. However, the operational complexity has been compounded by the absence of standardized data formats and the need to switch between various platforms for generating different Venn diagrams. To address these challenges, we introduce the EVenn platform, a versatile tool offering a unified interface for efficient data exploration and visualization of diverse Venn diagrams. EVenn (http://www.ehbio.com/test/venn) streamlines the data upload process with a standardized format, enhancing the capabilities for multimodule analysis. This comprehensive protocol outlines various applications of EVenn, featuring representative results of multiple Venn diagrams, data uploads in the centralized data center, and step-by-step case demonstrations. Through these functionalities, EVenn emerges as a valuable and user-friendly tool for the in-depth exploration of multiomics data.

Keywords: Euler diagram; UpSet plot; Venn network diagram; flower plot; interactive Venn diagram; multiomics data visualization; standardized data formats.

Figure 1

Representative result diagrams in EVenn. (A) Interactive Standard Venn diagrams for two to six sets. (B) Interactive Edwards diagrams for two to six sets. (C) Euler diagrams for two to three sets. (D) UpSet plot displaying empty intersections of five sets and nonempty intersections of seven sets. (E) Flower plot for 19 sets and 70 sets. (F) Venn network diagrams for four to five sets. (G) Interrelation among Venn diagram, UpSet plot, and Venn network.

Figure 2

Case demonstrations in EVenn. (A) Interactive Venn diagrams for differential metabolites of five parts of Poria cocos. (B) Interactive Edwards diagrams for differential metabolites of five parts of Poria cocos. (C) Euler diagrams for differentially expressed genes in three cell types following anticancer drug treatment. (D) UpSet plot for seven transcription regulators and their targeting genes in ChIP‐seq. (E) Interactive flower plot displaying 18 groups of common and unique elements of OTUs. (F) Interactive flower plot showcasing OTUs of common and after subtracting common elements in 18 groups. (G) Venn network diagrams for visualizing gene ontology enrichment analysis results for Andrographis paniculata. (H) Venn network diagram exclusively showcasing common and unique genes of four biological processes of Andrographis paniculata.