Update 10 files

- /Data Annotation/GO_enrichment/GO_molecular_function.png
- /Data Annotation/.gitkeep
- /Data Annotation/GO_enrichment/GO_cellular_component.png
- /Data Annotation/GO_enrichment/GO_biological_function.png
- /Data Annotation/GO_enrichment/biomart_for_annotation.R
- /Data Annotation/GO_enrichment/GO_enrichment.R
- /Data Annotation/GO_enrichment/GO molecular function.png
- /Data Annotation/GO_enrichment/GO biological function.png
- /Data Annotation/GO_enrichment/GO cellular component.png
- /Data Annotation/GO_enrichment/mrna.csv

Data Annotation/GO_enrichment/GO_enrichment.R

@@ -2,12 +2,11 @@ library(clusterProfiler)
 library(org.Hs.eg.db)
 library(AnnotationDbi)
 
-data <- read.table("C:/Users/Emre/Desktop/ensembl.txt", sep = "\n", header = TRUE)
+data <- read.csv("C:/Users/Emre/Desktop/go.csv", sep = ";", header = TRUE)
 
-genes_to_test <- data$ENSEMBLE_ID
+genes_to_test <- data$ensembl_gene_id
 
 GO_results <- enrichGO(gene = genes_to_test, OrgDb = "org.Hs.eg.db", keyType = "ENSEMBL", ont = "BP")
-
 as.data.frame(GO_results)
 
 fit <- plot(barplot(GO_results, showCategory = 15))
@@ -15,7 +14,6 @@ fit
 
 
 GO_results2 <- enrichGO(gene = genes_to_test, OrgDb = "org.Hs.eg.db", keyType = "ENSEMBL", ont = "MF")
-
 as.data.frame(GO_results2)
 
 fit2 <- plot(barplot(GO_results2, showCategory = 15))
@@ -23,7 +21,6 @@ fit2
 
 
 GO_results3 <- enrichGO(gene = genes_to_test, OrgDb = "org.Hs.eg.db", keyType = "ENSEMBL", ont = "CC")
-
 as.data.frame(GO_results3)
 
 fit3 <- plot(barplot(GO_results3, showCategory = 15))

Data Annotation/GO_enrichment/biomart_for_annotation.R

 library(biomaRt)
 ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
-gene_list <- c('RUVBL1', 'TRIP13', 'COL1A1', 'NDRG2', 'MCM2', 'DUOX1', 'FSCN1',
-               'TMPRSS11E', 'ANO1', 'IGFBP3', 'TIAM1', 'GPX3', 'HOPX', 'CFD',
-               'PPP1R3C', 'TMPRSS11D', 'COL5A2', 'IL1RN', 'LYPD3', 'SLURP1', 'MYH10',
-               'SERPINB2', 'TSPAN6', 'SIM2', 'ALOX12', 'TYMP', 'SPRR3', 'MMP10',
-               'ERCC3', 'EMP1', 'FLG', 'GABRP', 'GALE', 'GALNT1', 'HSPB8', 'HSPBAP1',
-               'HSPD1', 'ENTPD6', 'ACPP', 'AIM2', 'ALDH9A1', 'AQP3', 'ATP6V1D',
-               'ZNF185', 'CES2', 'CH25H', 'CLIC3', 'CYP4B1', 'CRISP3', 'CRNN')
+mrna <- read.csv("C:/Users/Emre/Desktop/mrna.csv")
+gene_list <- mrna$Gene_symbol
+gene_list
 
 ensembl_ids <- getBM(attributes = c("ensembl_gene_id", "external_gene_name"),
                      filters = "external_gene_name",
                      values = gene_list,
                      mart = ensembl)
 
-print(ensembl_ids)
\ No newline at end of file
+print(ensembl_ids)
+
+library(writexl)
+write_xlsx(ensembl_ids, path = "C:/Users/Emre/Desktop/go.csv")
+
+