clusterProfiler富集分析将ID转换为SYMBOL

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library(clusterProfiler)
library(org.Mm.eg.db)

> X <- bitr(gene, fromType='SYMBOL', toType='ENTREZID', OrgDb='org.Mm.eg.db')
> EGG <- enrichKEGG(gene= X$ENTREZID,
                  organism     = 'mmu',
                  pvalueCutoff = 0.05)
# 默认情况下，如果将EGG转为data.frame，ID这一行显示“ENTREZID”
> test <- data.frame(EGG)
	ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count
mmu04066	mmu04066	HIF-1 signaling pathway	11/171	114/8910	1.10E-05	0.002315845	0.002137347	228026/18127/14254/16828/11674/18641/11676/15251/112407/56421/22339	11
mmu00010	mmu00010	Glycolysis / Gluconeogenesis	8/171	67/8910	3.89E-05	0.00319374	0.002947578	14751/14447/16828/11674/18746/18641/11676/56421	8
mmu05230	mmu05230	Central carbon metabolism in cancer	8/171	69/8910	4.82E-05	0.00319374	0.002947578	228026/16828/18746/18641/80879/15251/56421/18596	8
mmu04015	mmu04015	Rap1 signaling pathway	14/171	214/8910	6.05E-05	0.00319374	0.002947578	14810/13636/14254/16542/244668/23880/29857/16415/240168/22339/18596/106952/20469/19395	14
mmu00030	mmu00030	Pentose phosphate pathway	5/171	33/8910	0.000377044	0.015911275	0.014684889	14751/11674/18641/11676/56421	5
mmu04330	mmu04330	Notch signaling pathway	6/171	54/8910	0.000551144	0.019381898	0.017888008	18128/433586/15214/16450/18131/18132	6

# 若需显示SYMBOL，使用如下命令：
> test <- setReadable(EGG, OrgDb = org.Mm.eg.db, keyType="ENTREZID")

ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count
mmu04066	HIF-1 signaling pathway	11/171	114/8910	1.10E-05	0.002315845	0.002137347	Pdk1/Nos3/Flt1/Ldha/Aldoa/Pfkl/Aldoc/Hif1a/Egln3/Pfkp/Vegfa	11
mmu00010	Glycolysis / Gluconeogenesis	8/171	67/8910	3.89E-05	0.00319374	0.002947578	Gpi1/Gapdhs/Ldha/Aldoa/Pkm/Pfkl/Aldoc/Pfkp	8
mmu05230	Central carbon metabolism in cancer	8/171	69/8910	4.82E-05	0.00319374	0.002947578	Pdk1/Ldha/Pkm/Pfkl/Slc16a3/Hif1a/Pfkp/Pdgfrb	8
mmu04015	Rap1 signaling pathway	14/171	214/8910	6.05E-05	0.00319374	0.002947578	Grin1/Efna1/Flt1/Kdr/Sipa1l2/Fyb/Mapk12/Itgb2l/Rasgrp3/Vegfa/Pdgfrb/Arap3/Sipa1/Rasgrp2	14
mmu00030	Pentose phosphate pathway	5/171	33/8910	0.000377044	0.015911275	0.014684889	Gpi1/Aldoa/Pfkl/Aldoc/Pfkp	5
mmu04330	Notch signaling pathway	6/171	54/8910	0.000551144	0.019381898	0.017888008	Notch1/Maml3/Hey2/Jag2/Notch3/Notch4	6
  • 本文作者：括囊无誉
  • 本文链接： RNASEQ/KEGG_ID_symbol/
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