1 Access gene information with biomaRt from ensembl database

library(biomaRt)
attributes <-  c(
    "chromosome_name",
    "start_position",
    "end_position",
    "strand",
    "ensembl_gene_id",
    "entrezgene_id",
    "external_gene_name"
)

1.1 Mouse

mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl")
mouse.genes <- getBM(attributes = attributes , mart = mouse)

## Cache found

# Show chromossome 1
DT::datatable(mouse.genes[mouse.genes$chromosome_name == "1",],filter =  "top")

1.2 Human

human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
human.genes <- getBM(attributes =  attributes, mart = human)

## Cache found

# Show chromossome 1
DT::datatable(human.genes[human.genes$chromosome_name == "1",],filter =  "top")

2 Comparing gene annotations

# Is there any overlap between symbols ?
count <- plyr::count(mouse.genes$external_gene_name %in% human.genes$external_gene_name)
colnames(count)[1] <- "Mouse Gene Symbol found also in Human gene symbols"
count

count <- plyr::count(human.genes$external_gene_name %in% mouse.genes$external_gene_name)
colnames(count)[1] <- "Human Gene Symbol found also in Mouse gene symbols"
count

# which ones overlap ?
count <- as.data.frame(mouse.genes$external_gene_name[which(mouse.genes$external_gene_name %in% human.genes$external_gene_name)])
colnames(count) <- "Overlapping gene names"
count

# Does ensembl_gene_id overlap ?
count <- plyr::count(mouse.genes$ensembl_gene_id %in% human.genes$ensembl_gene_id)
colnames(count)[1] <- "Mouse ENSEMBL Gene ID found also in Human ENSEMBL Gene ID"
count

count <- plyr::count(human.genes$ensembl_gene_id %in% mouse.genes$ensembl_gene_id)
colnames(count)[1] <- "Human ENSEMBL Gene ID found also in Mouse  ENSEMBL Gene ID"
count

Comparing human and mouse gene annotations

2019-08-08

1 Access gene information with biomaRt from ensembl database

1.1 Mouse

1.2 Human

2 Comparing gene annotations