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2 hours ago by

Germany

It is not uncommon that some genes do not have a HGNC symbol, especially non-coding genes.

symbol <- getBM(attributes = c("ensembl_gene_id","hgnc_symbol"),
                             mart = useMart("ensembl", dataset="hsapiens_gene_ensembl"))

## Almost 25000 Ensembl genes have no HGNC symbol
sum(symbol$ensembl_gene_id != "") ## 67159
sum(symbol$hgnc_symbol != "") ## 42848

enter image description here

Code for that plot:

library(biomaRt)
library(ggplot2)

symbol <- getBM(attributes = c("ensembl_gene_id","hgnc_symbol", "gene_biotype"),
                mart = useMart("ensembl", dataset="hsapiens_gene_ensembl"))

## Almost 25000 Ensembl genes have no HGNC symbol
sum(symbol$ensembl_gene_id != "") ## 67159
sum(symbol$hgnc_symbol != "") ## 42848

df <- data.frame(table(symbol[symbol$ensembl_gene_id != "" & 
                              symbol$hgnc_symbol == "",]$gene_biotype)) %>% arrange(Freq)
colnames(df) <- c("Gene_Biotype", "Number")

df$Gene_Biotype <- factor(df$Gene_Biotype, levels = df$Gene_Biotype)

ggplot(data=df, aes(x=Gene_Biotype, y=Number)) +
  geom_bar(stat="identity") + 
  coord_flip() + 
  ggtitle("Genes without HGNC symbol")

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modified 1 hour ago

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2 hours ago
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ATpoint34k



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