Welcome to ShinyGO! Just paste your gene list to get enriched GO terms and othe pathways for over 200 plant and animal species. In addition, it also produces
KEGG pathway diagrams with your genes highlighted, hierarchical clustering trees and networks summarizing
overlapping terms/pathways, protein-protein interaction networks, gene characterristics plots, and enriched promoter motifs. See example outputs below:
ShinyGO tries to match your species with the 115 archaeal, 1678 bacterial,
and 238 eukaryotic species in the
and send the genes. If it is running, please wait until it finishes. This can take 5 minutes, especially for the first time when iDEP downloads large annotation files.
A list of gene ids, separated by tab, space, comma or new line characters.
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 tree below, 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 represent a enriched GO term. Related GO terms are connected by a line, whose thickness reflect percent of overlapping genes. Size of the node corresponds to number of genes.
Through API access to STRING-db, we also retrieve protein-protein interaction (PPI) network. In addition to a static network image, users can also get access to an 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.
4/24/2018: V0.4 Add STRING API, KEGG diagram, tree display and network.
4/27/2018: V0.41 Change to ggplot2, add grid and gridExtra packages
4/30/2018: V0.42 changed figure configurations for tree.
Protein-protein interaction(PPIs) networks
By sending your genes to the STRING website,
shinyGO is retrieving a sub-network, calculating PPI enrichment,
and generating custom URLs to the STRING website containing your genes. This can take 5 minutes. Patience will pay off!