WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• WebGestalt is a widely used tool for gene list interpretation in large-scale -omics studies.
• Existing functionalities support multiple organisms, gene identifiers, and functional categories.
• There is a growing need for specialized tools to interpret phosphoproteomics data.

Purpose of the Study:

• To update and enhance the WebGestalt tool for broader applicability and improved user experience.
• To introduce phosphosite set analysis for identifying kinases from phosphoproteomics data.
• To improve the visualization and accessibility of enrichment analysis results.

Main Methods:

• Implemented phosphosite set analysis for kinase identification from phosphoproteomics data.
• Redesigned user interfaces and result visualizations for enhanced user-friendliness.
• Developed two methods to reduce redundancy between enriched gene sets.
• Introduced a web API and an R package (WebGestaltR) for programmatic access and local analysis.

Main Results:

• WebGestalt 2019 update supports 12 organisms, 342 gene identifiers, and 155,175 functional categories.
• New phosphoproteomics analysis enables identification of important kinases.
• Improved interactive and publication-ready figures enhance result comprehension.
• Enhanced programmatic access via web API and R package.

Conclusions:

• The updated WebGestalt tool provides a more comprehensive and user-friendly platform for -omics data interpretation.
• The addition of phosphoproteomics analysis addresses a critical need in the field.
• Enhanced visualization and accessibility features facilitate deeper understanding of enrichment results.