BED files with promoter regions and gene names

[Hamza Umut Karakurt]

Dear Sir/Madam,

I am Hamza Umut Karakurt from Gebze Technical University, Turkey.

I need a BED file which involves promoter regions (+1000 bp upstream) and corresponding genes.

I can download chromosomal locations as BED file but I cannot add corresponding genes.

Is there any way to do it?

Best regards,

Thank you.

[Bishwa Kiran]

Hi Hamza,

I an not sure what exactly you are looking for but this tool might help 

https://github.com/everestial/SmallTools/tree/master/GtfToTable

Thanks,

Bishwa K. 

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[Jairo Navarro Gonzalez]

Hello Hamza,

Thank you for using the UCSC Genome Browser and your inquiry.

I believe you want a way to link gene names to its corresponding promoter. I am assuming that you are using the Table Browser and are selecting the BED output format, which gives you an option to select chromosome locations upstream of genes by 1000 bases. Using the default position for hg19, I got the following BED output:

chr21    33031813    33032013    uc002yoz.1_up_200_chr21_33031814_r    0    -
chr21    33031734    33031934    uc002ypa.3_up_200_chr21_33031735_f    0    +

I assume you want a way to have the 4th column contain the gene symbol instead of the knownGene identifiers, e.g., uc002ypa.3, and want the more commonly known gene symbols like SOD1. Unfortunately, this will require a bit of scripting to make the modifications as we do not have a utility to accomplish the task and is beyond the scope of this mailing list.

However, you can obtain the mappings from knownGene identifiers and their gene names by using the related kgXref table and selecting the geneSymbol column. For example, the mapping from the example above would be:

#hg19.knownGene.name    hg19.kgXref.geneSymbol
uc002yoz.1    BC041449
uc002ypa.3    SOD1

Also, please feel free to search our mailing-list archives for further guidance:

https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
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Jairo Navarro 
UCSC Genomics Institute

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