Entering edit mode
blim4 • 0
Last seen 19 months ago
United Kingdom

Hi, I just wonder what KEGG is for? I did GO enrichment analysis and found significant biological processes. Are these two analyses related? What can I know from the enrichKEGG?


clusterProfiler enrichKEGG • 1.7k views
Entering edit mode
Guido Hooiveld ★ 3.8k
Last seen 1 day ago
Wageningen University, Wageningen, the …

The KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway database contains pathway maps for cellular and organismal functions.

enrichKEGG() is a function which allows you to find overrepresented KEGG categories (pathways) in a set of significantly regulated genes. I would say it is complementary to a GO enrichment analysis. The main difference is that genes belonging to the same GO category do not necessarily have to be connected through a set of reactions, whereas KEGG categories are representations of (mostly) biological metabolic or signalling transduction pathways, in which the genes are connected through reactions. Also, the coverage of GO is larger than KEGG, because GO annotations are also 'electronically' annotated (IEA evidence; annotations that are computationally, or automatically, assigned to gene products without further manual curation), whereas KEGG categories are usually are manually curated.

Similar to KEGG are for example the Reactome Pathway Database, and WikiPwathways. There is large overlap between these databases.


Login before adding your answer.

Traffic: 391 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6