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Scripts/Script15.R

+######################################################################################################################################################################################################
+anchor_breast<-read.csv("./Tables/Table10.csv")$Gene 
+anchor_colorectal<-read.csv("./Tables/Table11.csv")$Gene
+Candidate_Breast<-read.csv("./Tables/Table8.csv")$x
+Candidate_Colorectal<-read.csv("./Tables/Table9.csv")$x
+######################################################################################################################################################################################################
+### STRING based analysis
+library(STRINGdb)
+string_db <- STRINGdb$new(version="11", species=9606,score_threshold=900, input_directory="")
+proteins = string_db$get_proteins()
+proteins$protein_external_id = toupper(proteins$protein_external_id)
+
+PPIs = string_db$get_interactions(proteins$protein_external_id)
+PPIs$from = sub(".*[.]", '', PPIs$from)
+PPIs$to = sub(".*[.]", '', PPIs$to)
+x<-character(length(PPIs$from))
+y<-character(length(PPIs$to))
+for (i in 1:length(PPIs$from)){
+  x[i]<-proteins$preferred_name[which(proteins$protein_external_id==paste0("9606.",PPIs$from[i]))]
+  y[i]<-proteins$preferred_name[which(proteins$protein_external_id==paste0("9606.",PPIs$to[i]))]
+  print(i)
+}
+
+
+PPIs_breast2<-list()
+PPIs_colorectal<-list()
+
+STRING_breast<-c()
+for (i in 1:40){
+  selA<-intersect(which(x==as.character(anchor_breast[i])),which(PPIs$combined_score>950))
+  setA<-y[selA]
+
+  selB<-intersect(which(y==as.character(anchor_breast[i])),which(PPIs$combined_score>950))
+  setB<-x[selB]
+
+  PPIs_breast[[i]]<-unique(union(setA,setB))
+  STRING_breast<-c(STRING_breast,PPIs_breast[[i]])
+  print(paste(i,j))
+}
+unique(STRING_breast)
+intersect(unique(STRING_breast),Candidate_Breast)
+
+
+STRING_colorectal<-c()
+for (i in 1:43){
+  selA<-intersect(which(x==as.character(anchor_colorectal[i])),which(PPIs$combined_score>975))
+  setA<-y[selA]
+  
+  selB<-intersect(which(y==as.character(anchor_colorectal[i])),which(PPIs$combined_score>975))
+  setB<-x[selB]
+  
+  PPIs_colorectal[[i]]<-unique(union(setA,setB))
+  STRING_colorectal<-c(STRING_colorectal,unique(PPIs_colorectal[[i]]))
+}
+unique(STRING_colorectal)
+intersect(unique(STRING_colorectal),Candidate_Colorectal)
+######################################################################################################################################################################################################
+# BioGrid based
+PPI<-read.csv("./Tables/Table25.csv")
+PPI_breast1<-list()
+PPI_breast2<-list()
+PPI_colorectal<-list()
+
+BioGrid_breast<-c()
+for (i in 1:40){
+  selA<-which(as.character(PPI$Official.Symbol.Interactor.A)==as.character(anchor_breast[i]))
+  setA<-as.character(PPI$Official.Symbol.Interactor.B[selA])
+
+  selB<-which(as.character(PPI$Official.Symbol.Interactor.B)==as.character(anchor_breast[i]))
+  setB<-as.character(PPI$Official.Symbol.Interactor.A[selB])
+
+  PPI_breast[[i]]<-unique(union(setA,setB))
+  BioGrid_breast<-c(BioGrid_breast,PPI_breast[[i]])
+}
+unique(BioGrid_breast)
+intersect(unique(BioGrid_breast),Candidate_Breast)
+
+
+BioGrid_colorectal<-c()
+for (i in 1:43){
+  selA<-which(as.character(PPI$Official.Symbol.Interactor.A)==as.character(anchor_colorectal[i]))
+  setA<-as.character(PPI$Official.Symbol.Interactor.B[selA])
+  
+  selB<-which(as.character(PPI$Official.Symbol.Interactor.B)==as.character(anchor_colorectal[i]))
+  setB<-as.character(PPI$Official.Symbol.Interactor.A[selB])
+  
+  PPI_colorectal[[i]]<-unique(union(setA,setB))
+  BioGrid_colorectal<-c(BioGrid_colorectal,PPI_colorectal[[i]])
+  print(paste(i,j))
+}
+unique(BioGrid_colorectal)
+intersect(unique(BioGrid_colorectal),Candidate_Colorectal)
+
+######################################################################################################################################################################################################
+intersect(unique(STRING_breast),unique(BioGrid_breast))
+intersect(intersect(unique(STRING_breast),unique(BioGrid_breast)),Candidate_Breast)
+
+intersect(unique(STRING_colorectal),unique(BioGrid_colorectal))
+intersect(intersect(unique(STRING_colorectal),unique(BioGrid_colorectal)),Candidate_Colorectal)
+
+