Oncoprint shallow deletions

[Imran Noorani]

Hello,

 

I have been looking at TCGA data for low grade gliomas on Cbioportal. For some genes, I can see on the oncoprint there are deep deletions, but no shallow deletions. However when I go to ‘plots’, looking at copy number changes vs expression levels, I can see there are many shallow deletions for the same genes. Does this mean that the oncoprint is just not plotting shallow deletions? If so, is there a way that these can be displayed?

 

Many thanks,

Imran Noorani

-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

[Ritika Kundra]

Hi Imran,

For Shallow Deletions, you can use the OQL:

DATATYPES:HETLOSS

<GENE1> <GENE2> etc.

This should allow you to view shallow deletions in the oncoprint.

Thanks,

Ritika

[Nikolaus Schultz]

Another way of running the query is as follows:

PTEN: HOMDEL HETLOSS

Or 

PTEN: MUT HOMDEL HETLOSS

More details about the OncoQuery language are here:

http://www.cbioportal.org/onco_query_lang_desc.jsp

Niki.

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[Imran Noorani]

Hi Niki and Ritika,

 

I have another question – please can you tell what statistical test is applied when there is comparison for mutual exclusivity / co-occurrence of genetic alterations in cbioportal?

 

Many thanks,

Imran

[Imran Noorani]

Thank you!

Imran

 

From: Nikolaus Schultz <nsch...@gmail.com>
Date: Tuesday, November 28, 2017 at 9:04 PM
To: Ritika Kundra <ritika...@gmail.com>, Imran Noorani <i...@sanger.ac.uk>
Cc: cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>
Subject: Re: [cbioportal] Oncoprint shallow deletions

 

Another way of running the query is as follows:

[Ritika Kundra]

Hi Imran,

It’s Fisher’s exact test. You could refer to the paper: https://www.ncbi.nlm.nih.gov/pubmed/23550210 for further details.

Thanks,

Ritika

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[Imran Noorani]

Thank you Ritika

Imran 

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