Question: Mapping genome regions to gene symbols in two ways get weird results
0
gravatar for Na Sed
3.9 years ago by
Na Sed270
United States
Na Sed270 wrote:

I have some genome regions which I am gonna map them to gene symbols.

To do that there are two methods which have different result. I have mentioned one example below:

1) Using 'Homo.sapeins' package    

library(Homo.sapiens)
geneRanges <- function(db, column="ENTREZID")
{
  g <- genes(db, columns=column)
  col <- mcols(g)[[column]]
  genes <- granges(g)[rep(seq_along(g), elementLengths(col))]
  mcols(genes)[[column]] <- as.character(unlist(col))
  genes
}

gns <- geneRanges(Homo.sapiens, column="SYMBOL")

splitColumnByOverlap <-  function(query, subject, column="ENTREZID", ...)
{
  olaps <- findOverlaps(query, subject, ...)
  
  f1 <- factor(subjectHits(olaps), levels=seq_len(subjectLength(olaps)))
  
  splitAsList(mcols(query)[[column]][queryHits(olaps)], f1)
}

library(GenomicRanges)

cnv <- makeGRangesFromDataFrame(data.frame(chr="chr2", start=109993208, end=109993264))

gene.Symbol <- splitColumnByOverlap(gns, cnv, "SYMBOL")

The obtained gene symbol is 'SH3RF3'.

2) using 'biomaRt' package

library(GenomicRanges)
library(biomaRt)

mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
region <- "2:109993208:109993264"
gene.Symbol <- getBM(attributes = c("hgnc_symbol", "chromosome_name", "start_position","end_position"),
            filters = c("chromosomal_region"), values=region, mart=mart)


The obtained result is:

hgnc_symbol chromosome_name start_position end_position
1   LINC01123               2      109987063    109996140

Anyone knows why the results are different from each other?

Thanks.

ADD COMMENTlink modified 3.9 years ago by Devon Ryan89k • written 3.9 years ago by Na Sed270
3
gravatar for Devon Ryan
3.9 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

You're using two different genome versions. Biomart is giving you overlaps on GRCh38. The Homo.Sapiens package is giving you overlaps on GRCh37.

ADD COMMENTlink written 3.9 years ago by Devon Ryan89k

Oh, I didn't notice to it.

Do you know which of them is suitable for hg19? How can I find that?

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by Na Sed270

hg19 is GRCh37.

ADD REPLYlink written 3.9 years ago by Devon Ryan89k

How you know Homo.sapiens is GRCh37?

ADD REPLYlink written 3.9 years ago by Na Sed270

I looked at the genes overlapping the region you specified in GRCh37 and GRCh38. The results from those matched perfectly what you described. It's unfortunate that that R package doesn't mention its genome version.

ADD REPLYlink written 3.9 years ago by Devon Ryan89k

Thank you so much.

ADD REPLYlink written 3.9 years ago by Na Sed270
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