Retrieve All Genes Contained Within A Specific Chromosomal Region Using R And Biomart

Question

[secretjess]

EDIT: Now fixed, using filters = c("chromosome_name","start","end","biotype") instead. Question still stands though if anyone knows?

Original question: I've written some code which I think should take chromosomal coordinates (e.g. X:1-200000) and return protein coding genes (e.g. PLCXD1 and LINC00108) within that region on NCBI36.

I'm happy for it to return a gene only partially spanning the region or only genes contained entirely within that region at this stage, but I have no idea what it is actually returning.

Here's some simplified code of what I'm doing:

rm(list=ls())
library("biomaRt")
ensembl54=useMart("ENSEMBL_MART_ENSEMBL", host="may2009.archive.ensembl.org/biomart/martservice/", dataset="hsapiens_gene_ensembl")

chr.region = c("18:19092052-30289323","16:77462979-77500915","X:146419715-146584279","4:32776556-33393589","2:187947442-188506618")

entrez.ids=vector() 
entrez.count=vector()
all.results=data.frame() 

for (i in 1:length(chr.region)){
  filterlist=list(chr.region[i],"protein_coding")

  results=getBM(attributes = c("hgnc_symbol","entrezgene", "chromosome_name", "start_position", "end_position"), 
               filters = c("chromosomal_region","biotype"), 
               values = filterlist, 
               mart = ensembl54)

  results$region = chr.region[i]
  all.results=rbind(all.results,results)

  ids=unique(results$entrezgene) 
  ids <- ids[!is.na(ids)] 

  entrez.ids[i]=paste(ids, sep=",", collapse=",") 
  entrez.count[i]=unique(length(ids)) 
}

write.csv(all.results, file="all_results.csv",row.names=F)

Many thanks for any advice.

[Sudeep]

Could you post a few lines from the csv file that you are writing ?

[secretjess]

Hi Sudeep, here are two lines:

hgnc_symbol    entrezgene    chromosome_name    start_position    end_position    region
PARD6G    84552    18    76016114    76106388    18:19092052-30289323
ADNP2    22850    18    75967903    75999217    18:19092052-30289323

My question is now: if the imput region is between 19092052 and 30289323 why does the chromosomal_region filter return a gene at 75967903? Basically I am unsure what that filter is for and I'm just curious :)

[Giovanni M Dall'Olio]

Your code looks fine now that you have added the filters. Do you have any other doubt, or question?

[secretjess]

Thanks Giovanni - I'm just wondering what the chromosomal_region filter does?

Answer 1

[Sudeep]

Hi the issue was that chromosomal_region should be given as 18:19092052:30289323 and not 18:19092052-30289323

try this you will get the results you want

filterlist <- list("18:19092052:30289323","protein_coding")

results=getBM(attributes = c("hgnc_symbol","entrezgene", "chromosome_name", "start_position", "end_position"),filters = c("chromosomal_region","biotype"),values = filterlist, mart = ensembl54)

when you give incorrectly formatted chromosomal_region like 18:19092052-30289323 biomart takes the first value separated by ":" which in this case is 18 (chromosome) and returns all the protein coding genes on Chr.18

[secretjess]

Ahha, makes sense - many thanks! :)