WEB-based GEne SeT AnaLysis Toolkit
Translating gene lists into biological insights...

ORA Sample Run | GSEA Sample Run | NTA Sample Run | Phosphosite Sample Run (New in 2019!) | External Examples

| Manual | Citation | User Forum | GOView | WebGestaltR | WebGestalt 2017
Basic Parameters

Select Organism of Interest

Select Method of Interest

Select Functional Database

Select ID type category of the uploaded database

Select ID Type of the uploaded database

Upload Functional Database (max size: 5 MB)

Upload Database Description File
(optional, max size: 5 MB)

Gene List

Select Gene ID Type

Upload Gene List (max size: 5 MB)

Reference Gene List

Select Reference Set for Enrichment Analysis

Upload User Reference Set File (max size: 5 MB)
and Select ID Type

Advanced parameters

Minimum Number of Genes for a Category

Maximum Number of Genes for a Category

Multiple Test Adjustment

Significance Level


Number of Permutations

Collapse Method

Number of categories expected from set cover

Number of categories visualized in the report

Color in DAG

Continuous Binary

WebGestalt 2019 has been officially released with updated data. The 2017 version can be accessed through the link.

WebGestalt (WEB-based Gene SeT AnaLysis Toolkit) is a functional enrichment analysis web tool, which has on average 26,000 unique users from 144 countries and territories per year according to Google Analytics. The WebGestalt 2005, WebGestalt 2013 and WebGestalt 2017 papers have been cited in more than 2,500 scientific papers according to Google Scholar.

WebGestalt 2019 significantly improved the output report with emphasis on providing user-friendly interfaces which could directly translate into publication-ready figures. The R package WebGestaltR has been updated to work with the new verison, which provides an interface to integrate into other pipelines or run batch jobs locally. We also support loading data from third-party websites or services through an API to perform enrichment analysis. WebGestalt supports three well-established and complementary methods for enrichment analysis, including Over-Representation Analysis (ORA), Gene Set Enrichment Analysis (GSEA), and Network Topology-based Analysis (NTA).

Data sources for WebGestalt 2019 was updated on 01/14/2019, which supports 12 organisms, 354 gene identifiers from various databases and technology platforms, and 321,251 functional categories from public databases and computational analyses. Experimental data from organisms or with gene identifiers not covered by the WebGestalt database can also be analyzed in WebGestalt. We recently added phophosite data for kinase target enrichment analysis. Information in this version was collected from the following resources:

Browser support: We strongly recommend using evergreen browsers, such as Chrome and Firefox, although most functionalities should work on IE > 10. Version: fcc27621