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A hierarchical clustering tree summarizing the correlation among significant pathways listed in the Enrichment tab. Pathways with many shared genes are clustered together. Bigger dots indicate more significant P-values.

Figure

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Similar to the Tree tab, this interactive plot also shows the relationship between enriched pathways. Two pathways (nodes) are connected if they share 20% (default) or more genes. You can move the nodes by dragging them, zoom in and out by scrolling, and shift the entire network by click on an empty point and drag. Darker nodes are more significantly enriched gene sets. Bigger nodes represent larger gene sets. Thicker edges represent more overlapped genes.

Select KEGG pathways in the left to display your genes in pathway diagrams. Selected species only. Takes 1-3 minutes.

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If Gene Ontology is chosen, your genes are grouped by functional categories defined by high-level GO terms.

The characteristics of your genes are compared with the rest in the genome. Chi-squared and Student's t-tests are run to see if your genes have special characteristics when compared with all the other genes or, if uploaded, a customized background.

The genes are represented by red dots. The purple lines indicate regions where these genes are statistically enriched, compared to the density of genes in the background. We scanned the genome with a sliding window. Each window is further divided into several equal-sized steps for sliding. Within each window we used the hypergeometric test to determine if the presence of your genes are significant. Essentially, the genes in each window define a gene set/pathway, and we carried out enrichment analysis. The chromosomes may be only partly shown as we use the last gene's location to draw the line. Mouse over to see gene symbols. Zoom in regions of interest.

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The promoter sequences of your genes are compared with those of the other genes in the genome in terms of transcription factor (TF) binding motifs. "*Query gene" indicates a transcription factor coded by a gene included in your list.

Your genes are sent to STRING-db website for enrichment analysis and retrieval of a protein-protein network. We tries to match your species with the archaeal, bacterial, and eukaryotic species in the STRING server and send the genes. If it is running, please wait until it finishes. This can take 5 minutes, especially for the first time when shinyGO downloads large annotation files.

PPI network of DEGs

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For feedbacks, please contact us, or visit our homepage. For details, please see our paper and a detailed demo. ShinyGO shares many functionalities and databases with iDEP. Source code at GitHub.

Citation:
Ge SX, Jung D & Yao R, Bioinformatics 2020

Previous versions (still functional):
ShinyGO V0.65, based on database derived from Ensembl Release 103, archived on Oct. 15, 2021
ShinyGO V0.61, based on database derived from Ensembl Release 96, archived on May 23, 2020
ShinyGO V0.60, based on database derived from Ensembl BioMart version 96, archived on Nov 6, 2019
ShinyGO V0.51, based on database derived from Ensembl BioMart version 95, archived on May 20, 2019
ShinyGO V0.50, based on database derived from Ensembl BioMart version 92, archived on March 29, 2019
ShinyGO V0.41, based on database derived from Ensembl BioMart version 91, archived on July 11, 2018

Based on gene onotlogy (GO) annotation and gene ID mapping of 315 animal and plant genomes in Ensembl BioMart release 96 as of 5/20/2019. In addition, 115 archaeal, 1678 bacterial, and 238 eukaryotic genomes are annotated based on STRING-db v10. Additional pathway data are being collected for some model species from difference sources.

Genomes based on STRING-db is marked as STRING-db. If the same genome is included in both Ensembl and STRING-db, users should use Ensembl annotation, as it is more updated and is supported in more functional modules.

Sources for human pathway databases:

Sources for mouse pathway databases:

Input:

A list of gene ids, separated by tab, space, comma or the newline characters. Ensembl gene IDs are used internally to identify genes. Other types of IDs will be mapped to Ensembl gene IDs using ID mapping information available in Ensembl BioMart.

Output:

Enriched GO terms and pathways:


In addition to the enrichment table, a set of plots are produced. If KEGG database is choosen, then enriched pathway diagrams are shown, with user's genes highlighted, like this one below:


Many GO terms are related. Some are even redundant, like "cell cycle" and "cell cycle process". To visualize such relatedness in enrichment results, we use a hierarchical clustering tree and network. In this hierarchical clustering tree, related GO terms are grouped together based on how many genes they share. The size of the solid circle corresponds to the enrichment FDR.


In this network below, each node represents an enriched GO term. Related GO terms are connected by a line, whose thickness reflects percent of overlapping genes. The size of the node corresponds to number of genes.


Through API access to STRING-db, we also retrieve a protein-protein interaction (PPI) network. In addition to a static network image, users can also get access to interactive graphics at the www.string-db.org web server.


ShinyGO also detects transcription factor (TF) binding motifs enriched in the promoters of user's genes.

Changes:

6/6/2021: V0.66 Adjusted interface.

6/2/2021: V0.66 add customized background genes.

5/23/2021: V0.65 Database update to Ensembl 103 and STRING-db v11.

11/3/2019: V 0.61 Improved visualization based on suggestions from reviewers. Interactive networks.

5/20/2019: V0.60 Upgraded to Ensembl Biomart 96. Add annotation from STRING-db v10

3/29/2019: V0.51 Update annotation to Ensembl release 95. Interface change. Demo gene lists. Error messages.

9/10/2018: V0.5 Upgraded to Ensembl Biomart 92

4/30/2018: V0.42 changed figure configurations for tree.

4/27/2018: V0.41 Change to ggplot2, add grid and gridExtra packages

4/24/2018: V0.4 Add STRING API, KEGG diagram, tree display and network.