gene list

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andy stockbridge

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Mar 10, 2017, 3:30:43 PM3/10/17
to gen...@soe.ucsc.edu
Dear Team,

I have a long list of chr:position data (human) and would like to know which gene is it. Do you have this functionality (so I can upload a list) or can you recommend some other tools?
Thanks
Andy

Jairo Navarro Gonzalez

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Mar 16, 2017, 6:13:52 PM3/16/17
to andy stockbridge, UCSC Genome Browser Mailing List

Hello Andy,

Thank you for using the UCSC Genome Browser and your question about finding a gene using chr:position data.
To obtain your genes of interest by creating a custom track and using the Data Integrator to perform an intersection.
It may be helpful to review the Data Integrator user's guide.

First, create a custom track with the chr:position data file. 
For this example, the following position is the only entry in my custom track:

chr9 133265176 133275114

Then, navigate to the Data Integrator and select your favorite assembly:

clade: mammal
genome: Human
assembly: Dec. 2013 (GRCh38/hg38)
region to annotate: genome

Now, add your custom track:

group: Custom Tracks
track: User Track

Then, add your gene track of interest:

group: Genes and Gene Predictions
track: GENCODE v24

After your custom track and gene track have been added, under Output Options, click Choose fields...

A pop-up will appear and you will be able to select the fields that you are interested in. 
I will also add the related hg38.kgXref table to obtain the geneSymbol. 
For this example, I choose the following fields. 
User Track:
  • chrom
  • chromStart
  • chromEnd
GENCODE v24:
  • name
hg38.kgXref
  • geneSymbol

After you have selected the fields that you are interested in, click Done to exit the pop-up.
Once you are back on the main Data Integrator page, click get output.

You should get the following output in a new page (or file):

# hgIntegrator: database=hg38 region=genome Thu Mar 16 10:16:15 2017
#ct_UserTrack_3545.chrom    ct_UserTrack_3545.chromStart    ct_UserTrack_3545.chromEnd    knownGene.name    knownGene.kgXref_geneSymbol
chr9    133265176    133275114    uc064wtz.1    ABO
chr9    133265176    133275114    uc033djz.1    ABO
chr9    133265176    133275114    uc064wua.1    ABO

If you are new to the UCSC Genome Browser, you might also be interested in some introductory video tutorials available from our training page:
http://genome.ucsc.edu/training/index.html
http://www.openhelix.com/ucsc

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro 
UCSC Genomics Institute


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