WebGestalt: an integrated system for exploring gene sets in various biological contexts

By Bing Zhang, Stefan Kirov, Jay Snoddy. Nucleic Acids Res., 2005

1,886 citations recorded by the source corpus.

High-throughput technologies have led to the rapid generation of large-scale datasets about genes and gene products. These technologies have also shifted our research focus from ‘single genes’ to ‘gene sets’. We have developed a web-based integrated data mining system, WebGestalt (), to help biologists in exploring large sets of genes. WebGestalt is composed of four modules: gene set management, information retrieval, organization/visualization, and statistics. The management module uploads, saves, retrieves and deletes gene sets, as well as performs Boolean operations to generate the unions, intersections or differences between different gene sets. The information retrieval module currently retrieves information for up to 20 attributes for all genes in a gene set. The organization/visualization module organizes and visualizes gene sets in various biological contexts, including Gene Ontology, tissue expression pattern, chromosome distribution, metabolic and signaling pathways, protein domain information and publications. The statistics module recommends and performs statistical tests to suggest biological areas that are important to a gene set and warrant further investigation. In order to demonstrate the use of WebGestalt, we have generated 48 gene sets with genes over-represented in various human tissue types. Exploration of all the 48 gene sets using WebGestalt is available for the public at .

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/bbfb26b3e6595ea1518d82d712b2da08b5c48472

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Citations in the corpus

WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs (2019, methodology): “WebGestalt (WEB-based GEne SeT AnaLysis Toolkit) is one of the most widely used gene set enrichment analysis tools that help users extract biological insights from genes of interest (1).”
WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013 (2013, methodology): “In response to this critical need, in the 2005 NAR (Nucleic Acids Research) Web Server Issue, we presented WebGestalt (WEB-based GEne SeT AnaLysis Toolkit) (1), one of the ﬁrst software applications that integrate functional enrichment analysis and information visualization for the management, infor”
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases (2011, background): “A growing number of tools have been developed for pathway and disease identiﬁcation, including, but not limited to, MAPPFinder (13), EASE (14), DAVID (15,16), ArrayXPath (17), WebGestalt (18), FuncCluster (19), PageMan (20), GENECODIS (21,22), GeneTrail (23), g:Proﬁler (24), FunNet (25) and PaLS (26”
WGCNA: an R package for weighted correlation network analysis (2008, methodology): “Many gene ontology based functional enrichment analysis software programs such as David [40], AmiGO [41], Webgestalt [42] simply take lists of gene identifiers as input.”
Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges (2012, neutral): “edu/webgestalt/) [79]”
Temporal Control of Mammalian Cortical Neurogenesis by m6A Methylation (2017, positive): “2017 Zhang B, Kirov S, Snoddy J. WebGestalt: an integrated system for exploring gene sets in various biological contexts.”
GAGE: generally applicable gene set enrichment for pathway analysis (2009, neutral): “(Note that cutoff-based tools such as WebGestalt [13] and FatiScan [14] that apply Fisher's test and Hypergeometric test are sometimes denoted as gene set analysis tools.”
Using clusterProfiler to characterize multiomics data (2024, positive): “Although many software tools are available for enrichment analysis, they all have some limitations, such as Enrichr 30 , WebGestalt 31 and fgsea 32 , which do not support full-species analysis or the latest KEGG annotation updates.”
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists (2008, positive): “The WebGestalt, DAVID and Onto-Express groups independently reported their eﬀorts in detail, with the resulting collections including GeneKeyDB, the DAVID Knowledgebase and OT, respectively (65,87,88).”
GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists (2007, methodology): “A comparison of GENECODIS with related tools [1,22-25] and an example with test data [26] is provided in Additional data file 3.”
Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation (2010, methodology): “Tools such as Onto-Express [25], the Cytoscape [26] plugin BiNGO [27] and WebGestalt [28] display the hierarchical structure of enriched GO terms.”