question about comparing mutation status of another gene with OQL

[Ben H]

Hi community,

I was wondering how can I perform an expression comparison of gene A across disease types given that mutation profile of gene X has to be wildtype?

I have tried using OQL but in the standard boxplots view under Plots it said that "The results below are not filtered by the OQL specification from your query."

Or should I go about this via creating comparisons group?

Thank you!

Ben

[Zeynep Karagöz]

Hi Ben, 

Thanks for contacting us. 
You can perform the described filter following these steps: 

1- On the study view, go to the charts menu on the right and select "gene specific", "mutations" and "mutated vs not mutated" in the dropdown options as shown below:

2- Add chart and select the "non mutated" part in the newly created pie chart:

3- Apply filter and go to the plots tab to plot mRNA vs cancer type plot. This will be then only for the subset of the samples you filtered in the study view. 

Hope this helps. Please reply all if you have further questions so the community can follow up with you. 

Best,

Zeynep Karagöz

Data Engineer

E zey...@thehyve.nl

T +31 30 700 9713

M +31 627 121 63

W thehyve.nl

   

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[Ben H]

Thanks for the reply!

I noticed that for your step1, when I select "mutated vs not mutated", it only removes SNV/INDELs. Is there anyway to remove CNA and Fusion as well?

Thanks,

Ben

[Zeynep Karagöz]

Hi Ben, 

Yes, indeed the filter I have shown was for mutations only. To create a subset of samples without mutations+CNA+SVs you could add another plot for CNA data using the Gene Specific Charts option:

Then select both not mutated AND diploid samples using these charts. 

To also filter out SVs for the same gene, you can first save this sample subset as a group:

Then create a subset of this group with SV samples for the same gene using the SV table, find your gene of interest and add this filter to the sample population:

Create a new group with no mutations, no CNAs but with SVs. Then select the two groups you just created and go to the comparison view: 

If you now create a subgroup from non overlapping regions of the above plot, you will reach the desired population: no mutations, no CNAs and no SVs for the gene of interest. 

After having this group, you can click on "open in study view" and work with the desired subset of samples. 


Hope this helps. Let us know if you have any further questions. 

Best,

Zeynep Karagöz

Data Engineer

E zey...@thehyve.nl

T +31 30 700 9713

M +31 627 121 63

W thehyve.nl

   

To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/f7b666d2-cda1-41e3-b9ad-bc64b4ede0e9n%40googlegroups.com.

[Zeynep Karagöz]

Hi Ben, 

I am forwarding your message to the group. 
I am not sure I understand your question, but you can download the sample level data from the study view --> clinical data. 
You can also filter the clinical data table for the samples of interest by using the custom selection dropdown on the upper right corner. 

Let us know if you were referring to something else, please use reply all. 

Best,

Zeynep Karagöz

Data Engineer

E zey...@thehyve.nl

T +31 30 700 9713

M +31 627 121 63

W thehyve.nl

   

---------- Forwarded message ---------
From: Ben H <ban...@gmail.com>
Date: Tue, Jul 30, 2024 at 7:16 AM
Subject: Private message regarding: [cbioportal] question about comparing mutation status of another gene with OQL
To: Zeynep Karagöz <zey...@thehyve.nl>

Hi Zeynep,

Thanks for your help!

I have a follow question related to accessing the specimen id. Is there an easy way to download the comprehensive clinical information on per sample basis (rather than per patient).

For e.g. I ran into this question in pedcbioportal while checking "UM-Chor5C-CL-R4", it takes a couple of clicks to get to the SPECIMEN_ID "BS_CFSPNMKF".

Would there be a quicker way?

Regards,

Ben

[Ben H]

Hi cbioportal team,

Sorry maybe that wasn't a good example.  For the clinical data that I get from your approach, I would get some entries with multiple SPECIMEN_ID's as it is grouped by patient.

E.g. 7316-8716-WXS

returns SPECIMEN_ID: BS_K24D4BGK;BS_00FD2KMP

Whereas in the RNASeq data it is actually "BS_00FD2KMP" that is being used.

I can separate them offline via scripting, but is wondering if this can be done with the GUI.

Thanks again!

[de Bruijn, Ino]

Hi Ben,

 

Thanks for reaching out! I don’t fully understand the question unfortunately, could you elaborate what you’re seeing with screenshots?

 

Thanks so much!

Ino

 

From: cbiop...@googlegroups.com <cbiop...@googlegroups.com> on behalf of Ben H <ban...@gmail.com>
Date: Tuesday, July 30, 2024 at 2:10 PM
To: cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>
Subject: [EXTERNAL] Re: Private message regarding: [cbioportal] question about comparing mutation status of another gene with OQL

Hi cbioportal team, Sorry maybe that wasn't a good example. For the clinical data that I get from your approach, I would get some entries with multiple SPECIMEN_ID's as it is grouped by patient. E. g. 7316-8716-WXS returns SPECIMEN_ID: BS_K24D4BGK;BS_00FD2KMP

Hi cbioportal team,

 

Sorry maybe that wasn't a good example.  For the clinical data that I get from your approach, I would get some entries with multiple SPECIMEN_ID's as it is grouped by patient.

 

E.g. 7316-8716-WXS

returns SPECIMEN_ID: BS_K24D4BGK;BS_00FD2KMP

Whereas in the RNASeq data it is actually "BS_00FD2KMP" that is being used.

 

I can separate them offline via scripting, but is wondering if this can be done with the GUI.

 

Thanks again!

 

On Tuesday, July 30, 2024 at 9:30:24 AM UTC-4 Zeynep Karagöz wrote:

Hi Ben, 

I am forwarding your message to the group. 
I am not sure I understand your question, but you can download the sample level data from the study view --> clinical data. 
You can also filter the clinical data table for the samples of interest by using the custom selection dropdown on the upper right corner. 

Let us know if you were referring to something else, please use reply all. 

 

Best,

 

Zeynep Karagöz

Data Engineer

 

E zey...@thehyve.nl

T +31 30 700 9713

M +31 627 121 63

W thehyve.nl

   

 

 

---------- Forwarded message ---------
From: Ben H <ban...@gmail.com>
Date: Tue, Jul 30, 2024 at 7:16 AM
Subject: Private message regarding: [cbioportal] question about comparing mutation status of another gene with OQL
To: Zeynep Karagöz <zey...@thehyve.nl>

Hi Zeynep,

 

Thanks for your help!

 

I have a follow question related to accessing the specimen id. Is there an easy way to download the comprehensive clinical information on per sample basis (rather than per patient).

For e.g. I ran into this question in pedcbioportal while checking "UM-Chor5C-CL-R4", it takes a couple of clicks to get to the SPECIMEN_ID "BS_CFSPNMKF".

 

Would there be a quicker way?

 

Regards,

Ben

On Wednesday, July 24, 2024 at 5:09:04 AM UTC-4 Zeynep Karagöz wrote:

Hi Ben, 

 

Yes, indeed the filter I have shown was for mutations only. To create a subset of samples without mutations+CNA+SVs you could add another plot for CNA data using the Gene Specific Charts option:

Error! Filename not specified.

 

Then select both not mutated AND diploid samples using these charts. 

Error! Filename not specified.

To also filter out SVs for the same gene, you can first save this sample subset as a group:

Error! Filename not specified.

Then create a subset of this group with SV samples for the same gene using the SV table, find your gene of interest and add this filter to the sample population:

Error! Filename not specified.

Create a new group with no mutations, no CNAs but with SVs. Then select the two groups you just created and go to the comparison view: 

Error! Filename not specified.

Error! Filename not specified.

If you now create a subgroup from non overlapping regions of the above plot, you will reach the desired population: no mutations, no CNAs and no SVs for the gene of interest. 

Error! Filename not specified.

After having this group, you can click on "open in study view" and work with the desired subset of samples. 

Error! Filename not specified.

Hope this helps. Let us know if you have any further questions. 

 

Best,

 

Zeynep Karagöz

Data Engineer

 

E zey...@thehyve.nl

T +31 30 700 9713

M +31 627 121 63

W thehyve.nl

   

 

 

On Tue, Jul 23, 2024 at 5:08 PM Ben H <ban...@gmail.com> wrote:

Thanks for the reply!

I noticed that for your step1, when I select "mutated vs not mutated", it only removes SNV/INDELs. Is there anyway to remove CNA and Fusion as well?

 

Thanks,

Ben

 

On Tuesday, July 23, 2024 at 3:56:48 AM UTC-4 Zeynep Karagöz wrote:

Hi Ben, 

 

Thanks for contacting us. 
You can perform the described filter following these steps: 

1- On the study view, go to the charts menu on the right and select "gene specific", "mutations" and "mutated vs not mutated" in the dropdown options as shown below:

2- Add chart and select the "non mutated" part in the newly created pie chart:

3- Apply filter and go to the plots tab to plot mRNA vs cancer type plot. This will be then only for the subset of the samples you filtered in the study view. 

 

Hope this helps. Please reply all if you have further questions so the community can follow up with you. 

 

Best,

Zeynep Karagöz

Data Engineer

 

E zey...@thehyve.nl

T +31 30 700 9713

M +31 627 121 63

W thehyve.nl

   

 

 

 

On Tue, Jul 23, 2024 at 3:16 AM Ben H <ban...@gmail.com> wrote:

Hi community,

 

I was wondering how can I perform an expression comparison of gene A across disease types given that mutation profile of gene X has to be wildtype?

 

I have tried using OQL but in the standard boxplots view under Plots it said that "The results below are not filtered by the OQL specification from your query."

 

Or should I go about this via creating comparisons group?

 

Thank you!

Ben

--
You received this message because you are subscribed to the Google Groups "cBioPortal for Cancer Genomics Discussion Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cbioportal+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/eb48bf7b-daf7-4184-8d7c-0779ad334853n%40googlegroups.com.

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You received this message because you are subscribed to the Google Groups "cBioPortal for Cancer Genomics Discussion Group" group.
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To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/f7b666d2-cda1-41e3-b9ad-bc64b4ede0e9n%40googlegroups.com.

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