Commit 85adea50 authored by Sayed Rzgar Hosseini's avatar Sayed Rzgar Hosseini
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parent c0406a33
######################################################################################################################################################################################################
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)
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