Chapter 6 KEGG analysis
The annotation package, KEGG.db, is not updated since 2012. It’s now pretty old and in clusterProfiler, enrichKEGG (for KEGG pathway) and enrichMKEGG (for KEGG module) supports downloading latest online version of KEGG data for enrichment analysis. Using KEGG.db is also supported by explicitly setting use_internal_data parameter to TRUE, but it’s not recommended.
With this new feature, organism is not restricted to those supported in previous release, it can be any species that have KEGG annotation data available in KEGG database. User should pass 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".
clusterProfiler provides search_kegg_organism() function to help searching supported organisms.
## kegg_code scientific_name
## 366 ece Escherichia coli O157:H7 EDL933 (EHEC)
## common_name
## 366 <NA>## [1] 65 3## kegg_code scientific_name
## 361 eco Escherichia coli K-12 MG1655
## 362 ecj Escherichia coli K-12 W3110
## 363 ecd Escherichia coli K-12 DH10B
## 364 ebw Escherichia coli BW2952
## 365 ecok Escherichia coli K-12 MDS42
## 366 ece Escherichia coli O157:H7 EDL933 (EHEC)
## common_name
## 361 <NA>
## 362 <NA>
## 363 <NA>
## 364 <NA>
## 365 <NA>
## 366 <NA>6.1 KEGG over-representation test
data(geneList, package="DOSE")
gene <- names(geneList)[abs(geneList) > 2]
kk <- enrichKEGG(gene = gene,
organism = 'hsa',
pvalueCutoff = 0.05)
head(kk)## ID
## hsa04110 hsa04110
## hsa04114 hsa04114
## hsa04218 hsa04218
## hsa04061 hsa04061
## hsa03320 hsa03320
## hsa04914 hsa04914
## Description
## hsa04110 Cell cycle
## hsa04114 Oocyte meiosis
## hsa04218 Cellular senescence
## hsa04061 Viral protein interaction with cytokine and cytokine receptor
## hsa03320 PPAR signaling pathway
## hsa04914 Progesterone-mediated oocyte maturation
## GeneRatio BgRatio pvalue p.adjust
## hsa04110 11/93 124/7932 1.799177e-07 3.544378e-05
## hsa04114 10/93 128/7932 2.188761e-06 2.155930e-04
## hsa04218 10/93 160/7932 1.613634e-05 9.988265e-04
## hsa04061 8/93 100/7932 2.028074e-05 9.988265e-04
## hsa03320 7/93 76/7932 2.745818e-05 1.081852e-03
## hsa04914 7/93 99/7932 1.502807e-04 4.934216e-03
## qvalue
## hsa04110 3.465782e-05
## hsa04114 2.108123e-04
## hsa04218 9.766778e-04
## hsa04061 9.766778e-04
## hsa03320 1.057863e-03
## hsa04914 4.824802e-03
## geneID
## hsa04110 8318/991/9133/890/983/4085/7272/1111/891/4174/9232
## hsa04114 991/9133/983/4085/51806/6790/891/9232/3708/5241
## hsa04218 2305/4605/9133/890/983/51806/1111/891/776/3708
## hsa04061 3627/10563/6373/4283/6362/6355/9547/1524
## hsa03320 4312/9415/9370/5105/2167/3158/5346
## hsa04914 9133/890/983/4085/6790/891/5241
## Count
## hsa04110 11
## hsa04114 10
## hsa04218 10
## hsa04061 8
## hsa03320 7
## hsa04914 7Input ID type can be kegg, ncbi-geneid, ncbi-proteinid or uniprot, an example can be found in the post.
6.2 KEGG Gene Set Enrichment Analysis
kk2 <- gseKEGG(geneList = geneList,
organism = 'hsa',
nPerm = 1000,
minGSSize = 120,
pvalueCutoff = 0.05,
verbose = FALSE)
head(kk2)## ID Description setSize
## hsa04510 hsa04510 Focal adhesion 188
## hsa04151 hsa04151 PI3K-Akt signaling pathway 322
## hsa03013 hsa03013 RNA transport 131
## hsa05152 hsa05152 Tuberculosis 162
## hsa04062 hsa04062 Chemokine signaling pathway 165
## hsa04218 hsa04218 Cellular senescence 143
## enrichmentScore NES pvalue p.adjust
## hsa04510 -0.4188582 -1.706291 0.001430615 0.02322097
## hsa04151 -0.3482755 -1.497042 0.002614379 0.02322097
## hsa03013 0.4116488 1.735751 0.003095975 0.02322097
## hsa05152 0.3745153 1.630500 0.003154574 0.02322097
## hsa04062 0.3754101 1.633635 0.003184713 0.02322097
## hsa04218 0.4153718 1.772207 0.003194888 0.02322097
## qvalues rank leading_edge
## hsa04510 0.01576976 2183 tags=27%, list=17%, signal=23%
## hsa04151 0.01576976 1997 tags=23%, list=16%, signal=20%
## hsa03013 0.01576976 3383 tags=40%, list=27%, signal=29%
## hsa05152 0.01576976 2823 tags=34%, list=23%, signal=27%
## hsa04062 0.01576976 1298 tags=21%, list=10%, signal=19%
## hsa04218 0.01576976 1155 tags=17%, list=9%, signal=16%
## core_enrichment
## hsa04510 5595/5228/7424/1499/4636/83660/7059/5295/1288/23396/3910/3371/3082/1291/394/3791/7450/596/3685/1280/3675/595/2318/3912/1793/1278/1277/1293/10398/55742/2317/7058/25759/56034/3693/3480/5159/857/1292/3908/3909/63923/3913/1287/3679/7060/3479/10451/80310/1311/1101
## hsa04151 627/2252/7059/92579/5563/5295/6794/1288/7010/3910/3371/3082/1291/4602/3791/1027/90993/3441/3643/1129/2322/1975/7450/596/3685/1942/2149/1280/4804/3675/595/2261/7248/2246/4803/3912/1902/1278/1277/2846/2057/1293/2247/55970/5618/7058/10161/56034/3693/4254/3480/4908/5159/1292/3908/2690/3909/8817/9223/4915/3551/2791/63923/3913/9863/3667/1287/3679/7060/3479/80310/1311/5105/2066/1101
## hsa03013 10460/1978/55110/54913/9688/8894/11260/10799/9631/4116/5042/8761/6396/23165/8662/10248/55706/79833/9775/29107/23636/5905/9513/5901/10775/10557/4927/79902/1981/26986/11171/10762/8480/8891/11097/26019/10940/4686/9972/81929/10556/3646/9470/387082/1977/57122/8563/7514/79023/3837/9818/56000
## hsa05152 820/51806/6772/64581/3126/3112/8767/3654/1054/1051/3458/1520/11151/1594/50617/54205/91860/8877/3329/637/3689/7096/2207/3929/4360/5603/929/533/3452/6850/7124/1509/3569/7097/1378/8772/64170/3119/843/2213/8625/3920/2215/3587/5594/3593/9103/3592/6300/9114/10333/3109/3108/1432/3552
## hsa04062 3627/10563/6373/4283/6362/6355/2921/6364/3576/6352/10663/1230/6772/6347/6351/3055/1237/1236/4067/6354/114/3702/6361/1794/1234/6367/6375/6374/2919/409/4793/2792/6360/5880
## hsa04218 2305/4605/9133/890/983/51806/1111/891/993/3576/1978/898/9134/4609/1869/1029/22808/3804/1871/5499/91860/292/1019/11200/18756.3 KEGG Module over-representation test
KEGG Module is a collection of manually defined function units. In some situation, KEGG Modules have a more straightforward interpretation.