Functionalities

[Kinga Michalik]

Hi,

I have a question regarding new functionalities (or maybe old ones that I don't see?)

Would there be an option to:

1. do the reverse selection? For now I can only select samples with a desired mutation, but I cannot select samples that DO NOT contain this mutation. (I can select "currently unselected" but this applies to ALL previous selections and filters)

2. see the difference between samples that do not posses a mutation vs those that weren't profiled for the mutation?

3. see which samples actually have the mutation of interests? Now I see % and of course this can be done manually, but an option to download a table with samples/selected mutation would be just great.

My regards,

Kinga

[de Bruijn, Ino]

Hi Kinga,

 

Thanks for reaching out!

 

> 1. do the reverse selection? For now I can only select samples with a desired mutation, but I cannot select samples that DO NOT contain this mutation. (I can select "currently unselected" but this applies to ALL previous selections and filters)

 

On the Study View there is a new feature to add a gene chart and select wild type:

 

 

> 2. see the difference between samples that do not posses a mutation vs those that weren't profiled for the mutation?

 

There’s a few different places where profiling information is shown. On the Study View  you can select cases profiled for mutations:

 

 

The mutated genes frequencies are based on profiled samples only, see e.g.:

 

 

On the Results View, you can query for a gene and only include profiled samples:

 

 

Can give some more examples if helpful

 

> 3. see which samples actually have the mutation of interests? Now I see % and of course this can be done manually, but an option to download a table with samples/selected mutation would be just great.

 

If you are looking for this information for a few genes, you can query them and go to the download tab:

 

 

If you are looking for mutations across all genes, you can download all the files from a study from the datasets page:

 

https://www.cbioportal.org/datasets

 

Hope that helps!

Best wishes,

Ino

 

 

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