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## clusterProfiler v4.4.1 For help: https://yulab-smu.top/biomedical-knowledge-mining-book/
##
## If you use clusterProfiler in published research, please cite:
## T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation. 2021, 2(3):100141
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## Attaching package: 'clusterProfiler'
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## filter
## Loading required package: AnnotationDbi
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## Welcome to Bioconductor
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## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
## 'citation("Biobase")', and for packages 'citation("pkgname")'.
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## select
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library(ggplot2)
data(geneList, package="DOSE")
gene <- names(geneList)[abs(geneList) > 2]
gene.df <- bitr(gene, fromType = "ENTREZID",
toType = c("ENSEMBL", "SYMBOL"),
OrgDb = org.Hs.eg.db)
## 'select()' returned 1:many mapping between keys and columns
## Warning in bitr(gene, fromType = "ENTREZID", toType = c("ENSEMBL", "SYMBOL"), :
## 0.48% of input gene IDs are fail to map...
## ENTREZID ENSEMBL SYMBOL
## 1 4312 ENSG00000196611 MMP1
## 2 8318 ENSG00000093009 CDC45
## 3 10874 ENSG00000109255 NMU
## 4 55143 ENSG00000134690 CDCA8
## 5 55388 ENSG00000065328 MCM10
## 6 991 ENSG00000117399 CDC20
ego <- enrichGO(gene = gene,
universe = names(geneList),
OrgDb = org.Hs.eg.db,
ont = "CC",
pAdjustMethod = "BH",
pvalueCutoff = 0.01,
qvalueCutoff = 0.05,
readable = TRUE)
head(ego)
## ID Description GeneRatio
## GO:0005819 GO:0005819 spindle 26/201
## GO:0000775 GO:0000775 chromosome, centromeric region 19/201
## GO:0072686 GO:0072686 mitotic spindle 17/201
## GO:0000779 GO:0000779 condensed chromosome, centromeric region 16/201
## GO:0098687 GO:0098687 chromosomal region 23/201
## GO:0000776 GO:0000776 kinetochore 15/201
## BgRatio pvalue p.adjust qvalue
## GO:0005819 313/11865 1.748161e-11 5.261964e-09 4.802842e-09
## GO:0000775 169/11865 6.340879e-11 6.832630e-09 6.236463e-09
## GO:0072686 131/11865 6.809930e-11 6.832630e-09 6.236463e-09
## GO:0000779 123/11865 2.439813e-10 1.835960e-08 1.675767e-08
## GO:0098687 287/11865 5.709915e-10 3.437369e-08 3.137448e-08
## GO:0000776 115/11865 8.719737e-10 4.374401e-08 3.992722e-08
## geneID
## GO:0005819 CDCA8/CDC20/KIF23/CENPE/ASPM/DLGAP5/SKA1/NUSAP1/TPX2/TACC3/NEK2/CDK1/MAD2L1/KIF18A/BIRC5/KIF11/TRAT1/TTK/AURKB/PRC1/KIFC1/KIF18B/KIF20A/AURKA/CCNB1/KIF4A
## GO:0000775 CDCA8/CENPE/NDC80/TOP2A/HJURP/SKA1/NEK2/CENPM/CENPN/ERCC6L/MAD2L1/KIF18A/CDT1/BIRC5/EZH2/TTK/NCAPG/AURKB/CCNB1
## GO:0072686 KIF23/CENPE/ASPM/SKA1/NUSAP1/TPX2/TACC3/CDK1/MAD2L1/KIF18A/KIF11/TRAT1/AURKB/PRC1/KIFC1/KIF18B/AURKA
## GO:0000779 CENPE/NDC80/HJURP/SKA1/NEK2/CENPM/CENPN/ERCC6L/MAD2L1/KIF18A/CDT1/BIRC5/TTK/NCAPG/AURKB/CCNB1
## GO:0098687 CDCA8/CENPE/NDC80/TOP2A/HJURP/SKA1/NEK2/CENPM/RAD51AP1/CENPN/CDK1/ERCC6L/MAD2L1/KIF18A/CDT1/BIRC5/EZH2/TTK/NCAPG/AURKB/CHEK1/CCNB1/MCM5
## GO:0000776 CENPE/NDC80/HJURP/SKA1/NEK2/CENPM/CENPN/ERCC6L/MAD2L1/KIF18A/CDT1/BIRC5/TTK/AURKB/CCNB1
## Count
## GO:0005819 26
## GO:0000775 19
## GO:0072686 17
## GO:0000779 16
## GO:0098687 23
## GO:0000776 15
