DNA Methylation data from cbioportal

[Olga Cuenca]

Dear Sirs,

My name is Olga Cuenca, I am a PhD student from UNAM (Mexico). I would like to study DNA methylation levels in some genes in breast cancer.

I will appreciate a lot if you can inform me how to access to this data from the studies in your database.

Looking forward your reply

Thank you for your support.

Regards

M. Sc. Olga Cuenca

[Nikolaus Schultz]

Hi Olga,

We have methylation data for most TCGA studies. The provisional studies should all have it, as should some that match specific TCGA publications.

You cannot query based on methylation data, but you can visualize it on two places:

1: On the Plots tab, you can show the correlation between methylation and gene expression for specific genes

2: On the OncoPrint tab, you can add methylation and mRNA heat maps via the Heatmap menu

Note that cBioPortal only stores one methylation beta-value per gene and sample. We pick the one with the strongest negative correlation with the expression of the genes.

Niki.

 

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[Olga Cuenca]

Thank you very much for your support. 

This info is great.

Congratulations on the website.

Best regards

M. Sc. Olga Cuenca

El 21 may 2019, a las 10:31, Nikolaus Schultz <nsch...@gmail.com> escribió:

Hi Olga,

We have methylation data for most TCGA studies. The provisional studies should all have it, as should some that match specific TCGA publications.

You cannot query based on methylation data, but you can visualize it on two places:

1: On the Plots tab, you can show the correlation between methylation and gene expression for specific genes

2: On the OncoPrint tab, you can add methylation and mRNA heat maps via the Heatmap menu

Note that cBioPortal only stores one methylation beta-value per gene and sample. We pick the one with the strongest negative correlation with the expression of the genes.

Niki.

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