Get genomic coordinates from gene names

Question

[cameron.holman]

Hi All!

I am working in R with data extracted from EnsDb.Mmusculus.v95. I have generated a list of deferentially expressed genes and have their gene names like so:

...

Olfr61

P4ha2

Pcdh8

...

I am trying to create a data frame which maps each gene to its genomic coordinates like so:

...

Olfr61 Chr7:140637703-140638638

P4ha2 Chr11:54100924-54131668

Pcdh8 Chr14:79766775-79771312

...

I have started by using the GRanges function but am not finding it intuitive. This seems like it should be fairly simply. Any ideas?

After this I would like to plot each of these DE genes locations on a chromosome map to visualize if they are grouped in particular locations. Any favorite packages for doing this?

Thanks very much for your help

Answer 1

[Alex Reynolds]

No idea how to do it with R, but here's an approach with a couple, simple command-line statements:

$ wget -qO- ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_26/gencode.v26.basic.annotation.gff3.gz | gunzip -c > gencode.v26.basic.annotation.gff3
$ grep -wfF genes-of-interest.txt gencode.v26.basic.annotation.gff3 > genes-of-interest.gff3

Then munge genes-of-interest.gff3 for coordinates with awk.

Modify as needed for your source of annotations, genome assembly, etc.

[cameron.holman]

Thanks a lot for the response. I'll try working with this if I can't figure out how to run it in R. I am working with mmusculus v95 but should be able to tweak this for that purpose? Other issue is that I am running linux as a subsystem in windows (WSL, up to now just for running salmon/kallisto etc.) and don't have much experience with it.

[Alex Reynolds]

Gencode has mouse annotations.

Answer 2

[Emily]

BioMart is your easiest method. You can use it with an online interface but if you want to use R there's also an R package.