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Interpreting GO Enrichment Results. The Gene Ontology (GO) includes over tens of thousands of terms (functional categories), each tested individually for enrichment. These results are ranked, and only the top ones are displayed. Understanding this process is crucial for interpreting GO enrichment results.
- ShinyGO V0.51
3/29/2019: V.0.51, Annotation database updated. Welcome to...
- Xijin Ge
Dr. Ge's teaching and research focus on bioinformatics,...
- ShinyGO V0.41
Welcome to ShinyGO! Just paste your gene list to get...
- ShinyGO V0.51
ShinyGO is a web-based tool that analyzes gene lists and finds enriched GO terms, pathways, networks, and motifs for over 200 species. It also provides KEGG diagrams, STRING API, and gene characterization plots.
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".
Jul 5, 2023 · This tutorial explains how to perform Gene Ontology (GO) Enrichment Analysis using ShinyGO (a cloud R Shiny server). ShinyGO is an online graphical interface...
- 13 min
- 3.8K
- Ashok Kumar T
- 1 Introduction
- 2 Materials and Methods
- 3 Results
- 4 Discussion
- Acknowledgements
- GeneratedCaptionsTabForHeroSec
For a set of genes identified in genome-wide studies, enrichment analysis can be done to see if the set is enriched with genes of a certain pathway or functional category, such as those defined by gene ontology (GO) (Ashburner et al., 2000). Dozens of tools have been developed for enrichment analysis (Khatri et al., 2012). A small subset of these t...
ShinyGO is a Shiny application developed based on several R/Bioconductor packages, and a large annotation and pathway database compiled from many sources. See Supplementary Files S1 and S2 for more details. Source code is available at https://github.com/iDEP-SDSU/idep/tree/master/shinyapps/go61. Current database files are available at https://doi.o...
We developed ShinyGO for in-depth analysis of gene lists, with graphical visualization of enrichment, pathway, gene characteristics and protein interactions (Fig. 1). It is based on annotation databases for 315 organisms, including 184 at Ensembl (vertebrates, release 96) (Aken et al., 2017), 59 from Ensembl Plants (release 43) (Bolser et al., 2017...
ShinyGO is an intuitive, graphical tool for enrichment analysis. Even though its species coverage is not a broad as DAVID, ShinyGO has more comprehensive gene-sets regarding TF and miRNA target genes for human, mouse and Arabidopsis. We will continue to compile such information for other organisms and update the annotation database on a yearly basi...
The authors thank En Woo Sun, Brian Moore, Chad Julius, Luke Gassman, and Kevin Brandt for technical support, and Jianli Qi for compiling pathway databases.
ShinyGO is a web application that can help researchers gain insights from gene lists by linking them with molecular pathways and functional categories. It is based on a large annotation database and pathway databases from various sources, and provides graphical visualization of enrichment results and gene characteristics.
- Steven Xijin Ge, Dongmin Jung, Runan Yao
- 2020
ShinyGO is an intuitive, graphical tool for enrichment analysis. Even though its species coverage is not as broad as DAVID, ShinyGO has more comprehensive ge...
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Apr 25, 2023 · Gene ontology analysis is a powerful tool that enables researchers to uncover the biological function of genes, and it has become an essential component of g...
- 11 min
- 6.1K
- Genome Wide Study
