ESR1 Methylation data in breast cancer

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Lucas Porras

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Jul 13, 2021, 11:43:03 AMJul 13
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Hi, 

My name is Lucas Porras, I am a MSc student from University of Montreal and I am currently working on ESR1 gene DNA Methylation. I have been able to plot a figure for my gene of interest.
ESR1 DNA methylation plot .png
However, there are multiple regions methylated for that gene, I was wondering if you know which specific region is methylated ffrom that plot (HM450) ?
Looking forward to your reply. 

Thanks in advance for your help.

Regards 

Lucas Porras
M.Sc Student at the Institute for Research in Immunology and Cancer (IRIC)

Ino de Bruijn

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Jul 14, 2021, 12:48:57 PMJul 14
to Lucas Porras, cBioPortal for Cancer Genomics Discussion Group
Hi Lucas,

Thanks for reaching out!

Unfortunately we currently only capture methylation at the gene level, so we don't know the specific regions. If you look in the associated publication there might be more granular information available

Thanks,
Ino

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Nikolaus Schultz

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Jul 14, 2021, 2:10:02 PMJul 14
to Ino de Bruijn, Lucas Porras, cBioPortal for Cancer Genomics Discussion Group
Hi Lucas,

Just a little additional detail:

We pick one probe for each gene, based on correlation of the beta-value with the expression of the gene. See this FAQ item:

Unfortunately, we do not show the probe ID. You can however, dig up the original probe-level methylation data in the Broad Firehose data at this URL:

I hope this helps.
Niki.


On Jul 14, 2021, at 12:48 PM, Ino de Bruijn <i...@ino.pm> wrote:

Hi Lucas,

Thanks for reaching out!

Unfortunately we currently only capture methylation at the gene level, so we don't know the specific regions. If you look in the associated publication there might be more granular information available

Thanks,
Ino

On Tue, Jul 13, 2021 at 11:43 AM Lucas Porras <lucas.po...@gmail.com> wrote:
Hi, 

My name is Lucas Porras, I am a MSc student from University of Montreal and I am currently working on ESR1 gene DNA Methylation. I have been able to plot a figure for my gene of interest.
<ESR1 DNA methylation plot .png>
However, there are multiple regions methylated for that gene, I was wondering if you know which specific region is methylated ffrom that plot (HM450) ?
Looking forward to your reply. 

Thanks in advance for your help.

Regards 

Lucas Porras
M.Sc Student at the Institute for Research in Immunology and Cancer (IRIC)

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