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

By Yuxing Liao, Jing Wang, Eric J. Jaehnig, Zhiao Shi, Bing Zhang. Nucleic Acids Res., 2019

2,716 citations recorded by the source corpus.

Abstract WebGestalt is a popular tool for the interpretation of gene lists derived from large scale -omics studies. In the 2019 update, WebGestalt supports 12 organisms, 342 gene identifiers and 155 175 functional categories, as well as user-uploaded functional databases. To address the growing and unique need for phosphoproteomics data interpretation, we have implemented phosphosite set analysis to identify important kinases from phosphoproteomics data. We have completely redesigned result visualizations and user interfaces to improve user-friendliness and to provide multiple types of interactive and publication-ready figures. To facilitate comprehension of the enrichment results, we have implemented two methods to reduce redundancy between enriched gene sets. We introduced a web API for other applications to get data programmatically from the WebGestalt server or pass data to WebGestalt for analysis. We also wrapped the core computation into an R package called WebGestaltR for users to perform analysis locally or in third party workflows. WebGestalt can be freely accessed at http://www.webgestalt.org.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b3ecd09fe71587f583e84cedbd18b4629b4f17d1

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Citations in the corpus

Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches (2022, positive): “REAGENT or RESOURCE SOURCE IDENTIFIER GeneOntology (Ashburner et al., 2000) http://geneontology.org/ GraphPad Prism 9 GraphPad https://www.graphpad.com/ Harmony (Korsunsky et al., 2019) https://www.github.com/ immunogenomics/harmony Ilastik (Berg et al., 2019) https://www.ilastik.org/ ImageJ (Schnei”
WikiPathways: connecting communities (2020, methodology): “A number of R packages and online tools that perform enrichment analysis have incorporated WikiPathways into their methods and vignette examples, including g:Profiler (39), clusterProfiler (40), rSEA (41), Enrichr (42), IMPaLa (43) and WebGestalt (44).”
g:Profiler—interoperable web service for functional enrichment analysis and gene identifier mapping (2023 update) (2023, positive): “Previously, WebGestalt introduced two redundancy reduction methods in their w e b tool ( 6 ) cover determines the smallest gene set subset encompassing all genes from enriched sets, factoring in the P -value as the weight or cost of including a set.”
KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis (2021, background): “Therefore, several tools have provided downstream visualization of these enriched terms, including WebGestalt (29), Metascape (30), Enrichment map (31), WEGO (32) and GOPlot (33), in selecting and understanding the enriched results.”
WebGestalt 2024: faster gene set analysis and new support for metabolomics and multi-omics (2024, methodology): “To mitigate the issue of functionally similar enriched sets cluttering the output and reducing interpretability, we introduced a redundancy removal feature in WebGestalt 2019 ( 1 ,14 ).”