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. 2017 Jul 3;45(W1):W130-W137.
doi: 10.1093/nar/gkx356.

WebGestalt 2017: A More Comprehensive, Powerful, Flexible and Interactive Gene Set Enrichment Analysis Toolkit

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Free PMC article

WebGestalt 2017: A More Comprehensive, Powerful, Flexible and Interactive Gene Set Enrichment Analysis Toolkit

Jing Wang et al. Nucleic Acids Res. .
Free PMC article

Abstract

Functional enrichment analysis has played a key role in the biological interpretation of high-throughput omics data. As a long-standing and widely used web application for functional enrichment analysis, WebGestalt has been constantly updated to satisfy the needs of biologists from different research areas. WebGestalt 2017 supports 12 organisms, 324 gene identifiers from various databases and technology platforms, and 150 937 functional categories from public databases and computational analyses. Omics data with gene identifiers not supported by WebGestalt and functional categories not included in the WebGestalt database can also be uploaded for enrichment analysis. In addition to the Over-Representation Analysis in the previous versions, Gene Set Enrichment Analysis and Network Topology-based Analysis have been added to WebGestalt 2017, providing complementary approaches to the interpretation of high-throughput omics data. The new user-friendly output interface and the GOView tool allow interactive and efficient exploration and comparison of enrichment results. Thus, WebGestalt 2017 enables more comprehensive, powerful, flexible and interactive functional enrichment analysis. It is freely available at http://www.webgestalt.org.

Figures

Figure 1.
Figure 1.
Summary of the organisms, methods, functional categories, gene identifiers and interactive visualization and comparison features in WebGestalt 2017.
Figure 2.
Figure 2.
Enhanced interfaces and data visualization. (A) Tab-based output interface, (B) GO Slim classification plots, (C) interactive DAG visualization with nodes colored based on the direction and FDR values from enrichment analysis, (D) network visualization with nodes colored based on corresponding gene values.
Figure 3.
Figure 3.
Comparison of enriched GO terms among different cancer types. (A) Clickable Venn diagram. The clicked part can be highlighted by changing the edge color to red. (B) Interactive DAG visualization. Blue and red nodes in the DAG represent GO terms in the clicked part and other parts of the Venn diagram, respectively. Light blue nodes represent the ancestors and decedents of the selected node (‘Immune system process’ in this case) and blue edges represent the paths connecting these ancestors and decedents. (C) Sortable heat map. ‘Include’ and ‘Exclude’ check boxes are used for GO term selection and the excluded GO terms are blurred at the bottom of the heat map. (D) Selected GO terms in (C) are highlighted in blue in the DAG, and the common ancestor (i.e. organic acid metabolic process) of several highlighted terms were identified.

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