extract gene coordinates and TSS from gene list

Question

[Chironex]

Hi, I have a list of 50 genes like this:

"Tshz2"   "Ebf1"    "Col26a1" "Ebf2"    "Unc5c"   "Prkg1"   "Eya1"    "Ldb2"    "Rbms3"   "Arhgap6"

And I need the coordinates of gene body and the TSS +1000/-1000 bp. How can I get it on R? The genome is mm10.

Thanks

Answer 1

[Gordon Smyth]

To get gene bodies:

library(Rsubread)
GeneBody <- promoterRegions("mm10", upstream=0, downstream=Inf)

To get TSS +/- 1000 bp:

TSS <- promoterRegions("mm10", upstream=1000, downstream=1000)

This gives results for all genes by Entrez Gene ID.

[Chironex]

Thank you, this is perfect!!

Answer 2

[Trivas]

I always like using the UCSC Table Browser for things like these. You might need to convert to Refseq (NM_*) for it to work well, which can also be done easily with biomaRt.

Answer 3

[Carlo Yague]

I'm not going to give you a complete answer, but you can start looking at this posts: how to retrieve mouse (mm10) gene information from Ensemble using Biomart inR

And use the R interface for biomart. Its also possible to access biomart through the Ensemb website.

[Chironex]

thank you, I was able to get the coordinates of the gene, but I need to extract the TSS and extend it to 1000 bp.