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Copy pathDisease2Gene_OvaryCancer_lib.R
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207 lines (151 loc) · 13.1 KB
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set.seed(5081)
# Enrichment analysis libraries for OvaryCancer
# Load libraries
library(org.Hs.eg.db)
# Create gene ID mappings
entrezId_2_ensemblId <- as.data.frame(org.Hs.egENSEMBL)
entrezId_2_geneSymbol <- as.data.frame(org.Hs.egSYMBOL)
geneSymbol_2_ensemblId <- merge(entrezId_2_ensemblId, entrezId_2_geneSymbol, by = "gene_id")
## DisGeNET
DisGeNET_Disease2Gene_lib <- readRDS("InputFiles/Enrichment_analysis_libraries/DisGeNET_Disease2Gene_lib.rds")
DisGeNET_OvaryCancer2Gene_lib <- DisGeNET_Disease2Gene_lib[grep("ovary|ovarian|serous",
names(DisGeNET_Disease2Gene_lib),
ignore.case = TRUE)]
DisGeNET_OvaryCancer2Gene_lib <- DisGeNET_OvaryCancer2Gene_lib[grep("cancer|carcinoma|sarcoma",
names(DisGeNET_OvaryCancer2Gene_lib),
ignore.case = TRUE)]
DisGeNET_OvaryCancer2Gene_lib <- DisGeNET_OvaryCancer2Gene_lib[grep("hereditary|familial|susceptibility|predisposition",
names(DisGeNET_OvaryCancer2Gene_lib),
ignore.case = TRUE,
invert = TRUE)]
names(DisGeNET_OvaryCancer2Gene_lib) <- paste0(names(DisGeNET_OvaryCancer2Gene_lib), " [DisGeNET_curated]")
## OpenTargets
OpenTargets_Disease2Gene_GA_lib <- readRDS("InputFiles/Enrichment_analysis_libraries/OpenTargets_Disease2Gene_GA_lib.rds")
OpenTargets_OvaryCancer2Gene_GA_lib <- OpenTargets_Disease2Gene_GA_lib[grep("ovary|ovarian|serous",
names(OpenTargets_Disease2Gene_GA_lib),
ignore.case = TRUE)]
OpenTargets_OvaryCancer2Gene_GA_lib <- OpenTargets_OvaryCancer2Gene_GA_lib[grep("cancer|carcinoma|sarcoma",
names(OpenTargets_OvaryCancer2Gene_GA_lib),
ignore.case = TRUE)]
OpenTargets_OvaryCancer2Gene_GA_lib <- OpenTargets_OvaryCancer2Gene_GA_lib[grep("hereditary|familial|susceptibility|predisposition",
names(OpenTargets_OvaryCancer2Gene_GA_lib),
ignore.case = TRUE,
invert = TRUE)]
names(OpenTargets_OvaryCancer2Gene_GA_lib) <- paste0(names(OpenTargets_OvaryCancer2Gene_GA_lib), " [OpenTargets_GA]")
OpenTargets_Disease2Gene_RNA_lib <- readRDS("InputFiles/Enrichment_analysis_libraries/OpenTargets_Disease2Gene_RNA_lib.rds")
OpenTargets_OvaryCancer2Gene_RNA_lib <- OpenTargets_Disease2Gene_RNA_lib[grep("ovary|ovarian|serous",
names(OpenTargets_Disease2Gene_RNA_lib),
ignore.case = TRUE)]
OpenTargets_OvaryCancer2Gene_RNA_lib <- OpenTargets_OvaryCancer2Gene_RNA_lib[grep("cancer|carcinoma|sarcoma",
names(OpenTargets_OvaryCancer2Gene_RNA_lib),
ignore.case = TRUE)]
OpenTargets_OvaryCancer2Gene_RNA_lib <- OpenTargets_OvaryCancer2Gene_RNA_lib[grep("hereditary|familial|susceptibility|predisposition",
names(OpenTargets_OvaryCancer2Gene_RNA_lib),
ignore.case = TRUE,
invert = TRUE)]
names(OpenTargets_OvaryCancer2Gene_RNA_lib) <- paste0(names(OpenTargets_OvaryCancer2Gene_RNA_lib), " [OpenTargets_RNA]")
# OpenTargets_Disease2Gene_lit_lib <- readRDS("InputFiles/Enrichment_analysis_libraries/OpenTargets_Disease2Gene_lit_lib.rds")
# OpenTargets_OvaryCancer2Gene_lit_lib <- OpenTargets_Disease2Gene_lit_lib[grep("ovary|ovarian|serous",
# names(OpenTargets_Disease2Gene_lit_lib),
# ignore.case = TRUE)]
# OpenTargets_OvaryCancer2Gene_lit_lib <- OpenTargets_OvaryCancer2Gene_lit_lib[grep("cancer|carcinoma|sarcoma",
# names(OpenTargets_OvaryCancer2Gene_lit_lib),
# ignore.case = TRUE)]
# OpenTargets_OvaryCancer2Gene_lit_lib <- OpenTargets_OvaryCancer2Gene_lit_lib[grep("hereditary|familial|susceptibility|predisposition",
# names(OpenTargets_OvaryCancer2Gene_lit_lib),
# ignore.case = TRUE,
# invert = TRUE)]
# names(OpenTargets_OvaryCancer2Gene_lit_lib) <- paste0(names(OpenTargets_OvaryCancer2Gene_lit_lib), " [OpenTargets_literature]")
OpenTargets_Disease2Gene_SM_lib <- readRDS("InputFiles/Enrichment_analysis_libraries/OpenTargets_Disease2Gene_SM_lib.rds")
OpenTargets_OvaryCancer2Gene_SM_lib <- OpenTargets_Disease2Gene_SM_lib[grep("ovary|ovarian|serous",
names(OpenTargets_Disease2Gene_SM_lib),
ignore.case = TRUE)]
OpenTargets_OvaryCancer2Gene_SM_lib <- OpenTargets_OvaryCancer2Gene_SM_lib[grep("cancer|carcinoma|sarcoma",
names(OpenTargets_OvaryCancer2Gene_SM_lib),
ignore.case = TRUE)]
OpenTargets_OvaryCancer2Gene_SM_lib <- OpenTargets_OvaryCancer2Gene_SM_lib[grep("hereditary|familial|susceptibility|predisposition",
names(OpenTargets_OvaryCancer2Gene_SM_lib),
ignore.case = TRUE,
invert = TRUE)]
names(OpenTargets_OvaryCancer2Gene_SM_lib) <- paste0(names(OpenTargets_OvaryCancer2Gene_SM_lib), " [OpenTargets_SM]")
## Enrichr
Enrichr_Disease2Gene_GeoDiseaseSig_lib <- readRDS("InputFiles/Enrichment_analysis_libraries/Enrichr_Disease2Gene_GeoDiseaseSig_lib.rds")
Enrichr_GeoOvaryCancerSignatures_Up <- Enrichr_Disease2Gene_GeoDiseaseSig_lib$Up[grep("ovary|ovarian|serous",
names(Enrichr_Disease2Gene_GeoDiseaseSig_lib$Up),
ignore.case = TRUE)]
Enrichr_GeoOvaryCancerSignatures_Up <- Enrichr_GeoOvaryCancerSignatures_Up[grep("cancer|carcinoma|sarcoma",
names(Enrichr_GeoOvaryCancerSignatures_Up),
ignore.case = TRUE)]
Enrichr_GeoOvaryCancerSignatures_Up <- Enrichr_GeoOvaryCancerSignatures_Up[grep("hereditary|familial|susceptibility|predisposition",
names(Enrichr_GeoOvaryCancerSignatures_Up),
ignore.case = TRUE,
invert = TRUE)]
names(Enrichr_GeoOvaryCancerSignatures_Up) <- paste0(names(Enrichr_GeoOvaryCancerSignatures_Up), " [Enrichr_GeoDiseaseSig_Up]")
Enrichr_GeoOvaryCancerSignatures_Down <- Enrichr_Disease2Gene_GeoDiseaseSig_lib$Down[grep("ovary|ovarian|serous",
names(Enrichr_Disease2Gene_GeoDiseaseSig_lib$Down),
ignore.case = TRUE)]
Enrichr_GeoOvaryCancerSignatures_Down <- Enrichr_GeoOvaryCancerSignatures_Down[grep("cancer|carcinoma|sarcoma",
names(Enrichr_GeoOvaryCancerSignatures_Down),
ignore.case = TRUE)]
Enrichr_GeoOvaryCancerSignatures_Down <- Enrichr_GeoOvaryCancerSignatures_Down[grep("hereditary|familial|susceptibility|predisposition",
names(Enrichr_GeoOvaryCancerSignatures_Down),
ignore.case = TRUE,
invert = TRUE)]
names(Enrichr_GeoOvaryCancerSignatures_Down) <- paste0(names(Enrichr_GeoOvaryCancerSignatures_Down), " [Enrichr_GeoDiseaseSig_Down]")
# ## Intogen [NOT FOUND]
#
# Intogen_Disease2Gene_lib <- readRDS("InputFiles/Enrichment_analysis_libraries/Intogen_Disease2Gene_lib.rds")
# Intogen_OvaryCancer2Gene_lib <- Intogen_Disease2Gene_lib[grep("ovary|ovarian|serous", names(Intogen_Disease2Gene_lib),
# ignore.case = TRUE)]
# Intogen_OvaryCancer2Gene_lib <- Intogen_OvaryCancer2Gene_lib[grep("cancer|carcinoma|sarcoma",
# names(Intogen_OvaryCancer2Gene_lib),
# ignore.case = TRUE)]
# Intogen_OvaryCancer2Gene_lib <- Intogen_OvaryCancer2Gene_lib[grep("hereditary|familial|susceptibility|predisposition",
# names(Intogen_OvaryCancer2Gene_lib),
# ignore.case = TRUE,
# invert = TRUE)]
# names(Intogen_OvaryCancer2Gene_lib) <- paste0(names(Intogen_OvaryCancer2Gene_lib), " [Intogen]")
# ## PharmGKB [NOT FOUND]
#
# PharmGKB_Disease2Gene_lib <- readRDS("InputFiles/Enrichment_analysis_libraries/PharmGKB_Disease2Gene_lib.rds")
# PharmGKB_OvaryCancer2Gene_lib <- PharmGKB_Disease2Gene_lib[grep("ovary|ovarian|serous",
# names(PharmGKB_Disease2Gene_lib),
# ignore.case = TRUE)]
# PharmGKB_OvaryCancer2Gene_lib <- PharmGKB_OvaryCancer2Gene_lib[grep("cancer|carcinoma|sarcoma",
# names(PharmGKB_OvaryCancer2Gene_lib),
# ignore.case = TRUE)]
# PharmGKB_OvaryCancer2Gene_lib <- PharmGKB_OvaryCancer2Gene_lib[grep("hereditary|familial|susceptibility|predisposition",
# names(PharmGKB_OvaryCancer2Gene_lib),
# ignore.case = TRUE,
# invert = TRUE)]
# names(PharmGKB_OvaryCancer2Gene_lib) <- paste0(names(PharmGKB_OvaryCancer2Gene_lib), " [PharmGKB_associated]")
## ThETA
library(ThETA)
source("Scripts/ThETA/Corrected_Functions.R")
data(gtexv7_zscore)
data(ppi_strdb_700)
data(dis_vrnts)
data(disease_tissue_zscores)
data(centrality_score)
# compile the tissue-specific efficacy estimates of target(gene)-disease associations
OvaryCancer_genes = dis_vrnts[[which(names(dis_vrnts) == "EFO:0001075")]]
OvaryCancer_rel_tissue_scores = disease_tissue_zscores$z[which(rownames(disease_tissue_zscores$z) == "EFO:0001075"),]
OvaryCancer_Tscores <- tissue.specific.scores(disease_genes = OvaryCancer_genes$entrez,
ppi_network = ppi_strdb_700,
directed_network = FALSE,
tissue_expr_data = gtexv7_zscore,
dis_relevant_tissues = OvaryCancer_rel_tissue_scores,
W = centrality_score$borda.disc, selected_tissues = NULL,
cutoff = 4, verbose = TRUE)
ThETA_OvaryCancer2Gene_lib <- row.names(OvaryCancer_Tscores[order(OvaryCancer_Tscores$avg_tissue_score, decreasing = TRUE)[1:50],])
ThETA_OvaryCancer2Gene_lib <- list(entrezId_2_ensemblId[entrezId_2_ensemblId$gene_id %in% ThETA_OvaryCancer2Gene_lib, c("ensembl_id")])
names(ThETA_OvaryCancer2Gene_lib) <- paste0("Ovarian carcinoma (EFO_0001075)", " [ThETA]")
# Merge and save into one
Enrichment_OvaryCancer2Gene_lib <- c(DisGeNET_OvaryCancer2Gene_lib, OpenTargets_OvaryCancer2Gene_GA_lib,
OpenTargets_OvaryCancer2Gene_RNA_lib, OpenTargets_OvaryCancer2Gene_SM_lib,
Enrichr_GeoOvaryCancerSignatures_Up, Enrichr_GeoOvaryCancerSignatures_Down,
ThETA_OvaryCancer2Gene_lib)
# Save as RDS file
if(!dir.exists("InputFiles/Enrichment_analysis_libraries/")){dir.create("InputFiles/Enrichment_analysis_libraries/", recursive = TRUE)}
saveRDS(Enrichment_OvaryCancer2Gene_lib, "InputFiles/Enrichment_analysis_libraries/Disease2Gene_OvaryCancer_lib.rds")
print(warnings())