网络药理学—数据库获取疾病靶点并与中药靶点交集

rm(list = ls())
options(stringsAsFactors = F)

library(readxl)
library(RColorBrewer)
library(data.table)

#### Drug target
{
gene_drug_target_df <- read.table("table/target.csv",sep=",",header=T)
gene_drug_target <- c()
for (genes in gene_drug_target_df$Gene.Names){
  gene_drug_target <- c(gene_drug_target,strsplit(genes," ")[[1]])
}
gene_drug_target = unique(gene_drug_target)
}

#### Case target
{
##OMIM
gene_omim <- c()
gene_omim_df <- read_excel("table/case/OMIM-Gene-Map-Retrieval.xlsx")
for (genes in gene_omim_df$`Gene/Locus`){
  gene_omim <- c(gene_omim,strsplit(genes,",")[[1]])
}
gene_omim = unique(gene_omim)
length(gene_omim)
gene_omim <- gene_omim[!is.na(gene_omim)]
length(gene_omim)#211
gene_genecard <- gene_genecard[!is.na(gene_genecard)]
gene_disgnet <- gene_disgnet[!is.na(gene_disgnet)]


##Genecard
gene_genecard <- c()
gene_genecard_df <- fread("table/case/GeneCards-SearchResults.csv",data.table = F)
dim(gene_genecard_df)#1527    8
#筛选阈值1或者10
gene_genecard_df <- gene_genecard_df[gene_genecard_df$`Relevance score` > 1,]
dim(gene_genecard_df)#1473    8
gene_genecard =  unique(gene_genecard_df$`Gene Symbol`)
length(gene_genecard)
gene_genecard <- gene_genecard[!is.na(gene_genecard)]
length(gene_genecard)#1473



##Disgnet
gene_disgnet <- c()
gene_disgnet_df <- read_excel("table/case/DISEASES_Summary_GDA_CURATED_C3839507-C0085215-C0025322-C4552079.xlsx")
gene_disgnet = unique(gene_disgnet_df$gene)
length(gene_disgnet)
gene_disgnet <- gene_disgnet[!is.na(gene_disgnet)]
length(gene_disgnet)#141

## 数据库case target Venn
 {
      library(venn)
      gene_sets <- list(
        OMIM = gene_omim,
        GeneCards = gene_genecard,
        DisGeNET = gene_disgnet
      )
      mycol=c("#029149","#E0367A","#5D90BA","#431A3D","#91612D",
              "#FFD121","#D8D155","#223D6C","#D20A13","#088247",
              "#11AA4D","#7A142C","#5D90BA","#64495D","#7CC767")
      pdf(file="figure/venn_case_target_gene.pdf",width=5,height=5)

      venn(gene_sets,col=mycol[1:length(gene_sets)],zcolor=mycol[1:length(gene_sets)],box=F,ilabels = "counts")
      #在 line 参数中，负值会将标题向上移动，正值会向下移动。可以调整 line 的值，直到标题完全显示。
      title(main = "DOR Target Gene", cex.main = 1.5, font.main = 2, col.main = "black",line=-1)
      dev.off()
}

gene_case_target <- unique(c(gene_omim,gene_genecard,gene_disgnet))
length(gene_case_target)#1744
}


#### Drug target 与 Case target 交集

{
 
  Drug_case_target <- intersect(gene_drug_target,gene_case_target)
  length(Drug_case_target)#128
  #韦恩图
  gene_sets <- list(
    Drug_target = gene_drug_target,
    Case_target = gene_case_target
  )

  pdf(file="figure/venn_Drug_case_target.pdf",width=5,height=5)
  venn(gene_sets,col=mycol[1:length(gene_sets)],zcolor=mycol[1:length(gene_sets)],box=F,ilabels = "counts")
  title(main = "DOR Target Gene", cex.main = 1.5, font.main = 2, col.main = "black",line=-1)
  dev.off()
}

### 保存
write.csv(gene_drug_target,file = "../Table+Figure/T1.drug_target_gene.csv")
write.csv(gene_case_target,file = "../Table+Figure/T2.case_target_gene.csv")
write.csv(Drug_case_target,file = "../Table+Figure/T3.drug_case_target_intersect.csv")
save(gene_drug_target,gene_case_target,Drug_case_target,file = "Rdata/Drug_case_target.Rdata")