The KEGG FTP service has not been freely available for academic use since 2012, and there are many software packages using outdated KEGG annotation data. The clusterProfiler package supports downloading the latest online version of KEGG data using the KEGG website, which is freely available for academic users. Both KEGG pathways and modules are supported in clusterProfiler.
5.1 Supported organisms
The clusterProfiler package supports all organisms that have KEGG annotation data available in the KEGG database. Users should pass an abbreviation of academic name to the organism parameter. The full list of KEGG supported organisms can be accessed via http://www.genome.jp/kegg/catalog/org_list.html. KEGG Orthology (KO) Database is also supported by specifying organism = "ko".
The clusterProfiler package provides the search_kegg_organism() function to help search for supported organisms.
category
hsa04110 Cellular Processes
hsa04114 Cellular Processes
hsa04218 Cellular Processes
hsa04061 Environmental Information Processing
hsa03320 Organismal Systems
hsa04814 Cellular Processes
subcategory ID
hsa04110 Cell growth and death hsa04110
hsa04114 Cell growth and death hsa04114
hsa04218 Cell growth and death hsa04218
hsa04061 Signaling molecules and interaction hsa04061
hsa03320 Endocrine system hsa03320
hsa04814 Cell motility hsa04814
Description
hsa04110 Cell cycle
hsa04114 Oocyte meiosis
hsa04218 Cellular senescence
hsa04061 Viral protein interaction with cytokine and cytokine receptor
hsa03320 PPAR signaling pathway
hsa04814 Motor proteins
GeneRatio BgRatio RichFactor FoldEnrichment zScore pvalue
hsa04110 15/107 158/9522 0.09493671 8.448480 10.064414 2.064405e-10
hsa04114 10/107 139/9522 0.07194245 6.402205 6.839599 3.346185e-06
hsa04218 10/107 157/9522 0.06369427 5.668195 6.287354 9.939099e-06
hsa04061 8/107 100/9522 0.08000000 7.119252 6.557674 1.545425e-05
hsa03320 7/107 76/9522 0.09210526 8.196508 6.714716 2.147577e-05
hsa04814 10/107 197/9522 0.05076142 4.517292 5.317900 7.035033e-05
p.adjust qvalue
hsa04110 7.204774e-08 NA
hsa04114 5.839093e-04 NA
hsa04218 1.156249e-03 NA
hsa04061 1.348383e-03 NA
hsa03320 1.499009e-03 NA
hsa04814 4.092044e-03 NA
geneID
hsa04110 890/891/9212/7272/9133/9319/4085/81620/991/10403/1111/983/9232/4174/8318
hsa04114 891/3708/51806/9133/4085/6790/5241/991/983/9232
hsa04218 890/891/776/2305/3708/51806/9133/4605/1111/983
hsa04061 6373/6355/6362/1524/10563/3627/9547/4283
hsa03320 9415/5105/5346/3158/2167/4312/9370
hsa04814 10112/9493/81930/146909/24137/4629/3833/7802/1062/3832
Count
hsa04110 15
hsa04114 10
hsa04218 10
hsa04061 8
hsa03320 7
hsa04814 10
Input ID type can be kegg, ncbi-geneid, ncbi-proteinid or uniprot (see also Section 17.1.2). Unlike enrichGO(), there is no readable parameter for enrichKEGG(). However, users can use the setReadable() function, see also Section 17.2, if there is an OrgDb available for the species.
The enrichplot package implements several methods to visualize enriched terms. Most of them are general methods that can be used on GO, KEGG, MSigDb, and other gene set annotations. Here, we introduce the clusterProfiler::browseKEGG() and pathview::pathview() functions to help users explore enriched KEGG pathways with genes of interest.
To view the KEGG pathway, users can use the browseKEGG() function, which will open a web browser and highlight enriched genes.
(ref:pathviewscap) Visualize selected KEGG pathway by pathview().
(ref:pathviewcap) Visualize selected KEGG pathway by pathview(). Gene expression values can be mapped to gradient color scale.
(ref:pathviewcap)
References
Luo, Weijun, and Cory Brouwer. 2013. “Pathview: An R/Bioconductor Package for Pathway-Based Data Integration and Visualization.”Bioinformatics 29 (July): 1830–31. https://doi.org/10.1093/bioinformatics/btt285.
Yu, Guangchuang, Le-Gen Wang, Yanyan Han, and Qing-Yu He. 2012. “clusterProfiler: An r Package for Comparing Biological Themes Among Gene Clusters.”OMICS: A Journal of Integrative Biology 16 (5): 284–87. https://doi.org/10.1089/omi.2011.0118.
