extract gene coordinates and TSS from gene list
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14 months ago
Chironex ▴ 40

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

r genomicranges • 1.5k views
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14 months ago
Gordon Smyth ★ 7.2k

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.

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Thank you, this is perfect!!

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14 months ago
Trivas ★ 1.8k

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.

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14 months ago

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.

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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.

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