RE: [genome-cancer] small help

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Vizeacoumar, Frederick

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Aug 10, 2016, 2:00:27 PM8/10/16

to gen...@soe.ucsc.edu

Hi there,

I’d like to download the chromosome number, start base pair, end base pair, cytogenetic band Name, cytogenetic band start base pair, cytogenetic band end base pair and gene names including their start and end base pair location.

When I contacted helpdesk at Xena Browser, they asked me to get in touch with you because the Table browser they pointed to does not give the gene name but gieStain which I don’t know how to map it to gene name.

I’d like to map the CNV from the TCGA data to each chromosome and do further clustering to get a better idea. So, I’d really appreciate if you can help me.

Thanks,

Frederick

Frederick S. Vizeacoumar,

Research Officer,

Division of Oncology,

University of Saskatchewan,

4D01.5 Health Sciences Building,

Saskatoon.

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From: Mary Goldman [mailto:ma...@soe.ucsc.edu]
Sent: Thursday, August 04, 2016 4:32 PM
To: Vizeacoumar, Frederick <frederick....@usask.ca>; genome...@soe.ucsc.edu
Subject: Re: [genome-cancer] small help

Hi Frederick,

Oh I see! Sorry, I missed the mapping of gene names to these chromosomal locations. In this case I would recommend using the UCSC Genome Browser to obtain this. Their email is: gen...@soe.ucsc.edu

I am ccing our private mailing list so that my answers are recorded for our grant reporting purposes.

Best,
Mary
-------------
Mary Goldman
UCSC Xena Browser
http://xena.ucsc.edu/

---------- Forwarded message ----------
From: Vizeacoumar, Frederick <frederick....@usask.ca>
Date: Thu, Aug 4, 2016 at 1:57 PM
Subject: RE: [genome-cancer] small help
To: Mary Goldman <ma...@soe.ucsc.edu>

HI Mary,

Thank you very much for your reply. I was not feeling good last week and so I couldn’t reply to your email.

I noticed that the link generated Chromosome to its corresponding p and q arm and their cytoband location but I have no idea how to map the gieStain to the corresponding gene name that is present in the CNV of TCGA database.

Thanks for your help.

Cheers,

Frederick

Frederick S. Vizeacoumar,

Research Officer,

Division of Oncology,

University of Saskatchewan,

4D01.5 Health Sciences Building,

Saskatoon.

From: Mary Goldman [mailto:ma...@soe.ucsc.edu]
Sent: Tuesday, July 26, 2016 2:12 PM
To: Vizeacoumar, Frederick <frederick....@usask.ca>
Cc: genome...@soe.ucsc.edu
Subject: Re: [genome-cancer] small help

Hi Frederick,

You will want to download this data from the UCSC Genome Browser. The download is at the Table Browser here: http://genome.ucsc.edu/cgi-bin/hgTables?clade=mammal&org=Human&db=hg19&hgta_group=map&hgta_track=cytoBandIdeo

Note this is for hg19, which is what the TCGA data is mapped to.

Best,
Mary
-------------
Mary Goldman
UCSC Xena Browser
http://xena.ucsc.edu/

---------- Forwarded message ----------
From: Vizeacoumar, Frederick <frederick....@usask.ca>
Date: Tue, Jul 26, 2016 at 10:32 AM
Subject: [genome-cancer] small help
To: "genome...@soe.ucsc.edu" <genome...@soe.ucsc.edu>

Hi there,

I would like to download chromosome number, start base pair, end base pair, cytogenetic band Name, cytogenetic band start base pair, cytogenetic band end base pair and gene names including their start and end base pair location.

I know you use this information to plot the TCGA data but to further do some clustering, I need to know this information so I can cluster them by regions on each chromosome.

Thank you.

Regards,

Frederick

Frederick S. Vizeacoumar,

Research Officer,

Division of Oncology,

University of Saskatchewan,

4D01.5 Health Sciences Building,

Saskatoon.

Matthew Speir

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Aug 10, 2016, 3:43:16 PM8/10/16

to Vizeacoumar, Frederick, gen...@soe.ucsc.edu

Hi Frederick,

Thank you for your question about obtaining information on gene and cytogenetic band information from the UCSC Genome Browser.

The Data Integrator would be better suited to your request as it allows you to output data from multiple tracks simultaneously based on their intersection.

You can get the information you're interested in using the following steps:

1. Navigate to the Data Integrator, https://genome.ucsc.edu/cgi-bin/hgIntegrator.

2. Under the "Select Genome Assembly and Region" section, make the following selections:
    group: mammal
    genome: Human
    assembly: Feb 2009 (GRCh37/hg19)
    region to annotate: can choose between a single position, a list of genomic regions, or genome-wide

3. Under the "Configure Data Sources" section, make the following selection
    a. First, add the "Chromosome Band" track to the data sources section:
        track group: Mapping and Sequencing
        track: Chromosome Band

        Click "Add"

    b. Then add the "UCSC Genes" track to the data sources section:
        track group: Genes and Gene Predictions
        track: UCSC Genes

        Click "Add"

4. Click "Choose fields..."

5. Under the "Chromosome Band (cytoBand)" section, check the boxes next to chrom, chromStart, chromEnd, name.

6. Under the "UCSC Genes (knownGene)" section, check the boxes next to name, strand, txStart, txEnd.

7. Under the "UCSC Genes (knownGene)" section, choose "hg19.kgXref" from the drop-down menu under "Related tables" and click "Add table". Then check the box next to geneSymbol.

8. Click "Done".

9. Click "Get output".

Your output should look like this:

#cytoBand.chrom	cytoBand.chromStart	cytoBand.chromEnd	cytoBand.name	knownGene.name	knownGene.strand	knownGene.txStart	knownGene.txEnd	knownGene.kgXref_geneSymbol
chr21	31500000	35800000	q22.11	uc002yoz.1	-	33026870	33031813	BC041449
chr21	31500000	35800000	q22.11	uc002ypa.3	+	33031934	33041243	SOD1

For more information on using the Data Integrator, see our help page: https://genome.ucsc.edu/goldenPath/help/hgIntegratorHelp.html.

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.

Matthew Speir
UCSC Genome Bioinformatics Group