library(TCMDATA)
herbs <- c("灵芝")
lz <- search_herb(herb = herbs, type = "Herb_cn_name")
head(lz)## herb molecule target
## 1 lingzhi 3,4-Dihydroxybenzoic acid GAA
## 2 lingzhi 3,4-Dihydroxybenzoic acid POLB
## 3 lingzhi 3,4-Dihydroxybenzoic acid APP
## 4 lingzhi 3,4-Dihydroxybenzoic acid CA1
## 5 lingzhi 3,4-Dihydroxybenzoic acid CA12
## 6 lingzhi 3,4-Dihydroxybenzoic acid CA14
genes <- c("TP53", "EGFR", "BRCA1")
herbs <- search_target(genes)
head(herbs)## herb molecule target
## 1 fengmi Formic Acid TP53
## 2 jiuxiangchong 1,2-Benzenediol EGFR
## 3 fengfang Gallic Acid EGFR
## 4 fengfang Gallic Acid TP53
## 5 fengmi Gallic Acid EGFR
## 6 fengmi Gallic Acid TP53
# You may obtain your genes of interest by `intersect(lz$target, DE_genes)`
set.seed(2025)
g <- sample(lz$target, 200)
library(clusterProfiler)
x <- enrichGO(g, ont="MF", OrgDb='org.Hs.eg.db', keyType="SYMBOL")##
head(x)## ID Description
## GO:0004715 GO:0004715 non-membrane spanning protein tyrosine kinase activity
## GO:0035401 GO:0035401 histone H3Y41 kinase activity
## GO:0140801 GO:0140801 histone H2AXY142 kinase activity
## GO:0008353 GO:0008353 RNA polymerase II CTD heptapeptide repeat kinase activity
## GO:0032813 GO:0032813 tumor necrosis factor receptor superfamily binding
## GO:0035173 GO:0035173 histone kinase activity
## GeneRatio BgRatio RichFactor FoldEnrichment zScore pvalue
## GO:0004715 3/50 45/18639 0.06666667 24.85200 8.308092 0.0002380769
## GO:0035401 4/50 115/18639 0.03478261 12.96626 6.675697 0.0002544242
## GO:0140801 4/50 115/18639 0.03478261 12.96626 6.675697 0.0002544242
## GO:0008353 2/50 10/18639 0.20000000 74.55600 12.066463 0.0003130327
## GO:0032813 3/50 50/18639 0.06000000 22.36680 7.846087 0.0003257581
## GO:0035173 6/50 360/18639 0.01666667 6.21300 5.179876 0.0003863503
## p.adjust qvalue geneID Count
## GO:0004715 0.01938191 0.01497955 FYN/PTK2/PRKCD 3
## GO:0035401 0.01938191 0.01497955 ERBB2/FYN/PTK2/PRKCD 4
## GO:0140801 0.01938191 0.01497955 ERBB2/FYN/PTK2/PRKCD 4
## GO:0008353 0.01938191 0.01497955 CDK1/MAPK1 2
## GO:0032813 0.01938191 0.01497955 FASLG/RIPK1/TNF 3
## GO:0035173 0.01938191 0.01497955 ERBB2/FYN/CDK1/PTK2/PRKCD/RIPK1 6
library(enrichplot)
cnetplot(x)