Ramya Madupuri, How to import Microbiome data into cBioportal?

[Harry Sun]

Hi Ramya,

I am interested in importing microbiome data to cBioportal.I found your post https://github.com/cBioPortal/datahub/pull/1156. Can you give me the instruction and example including meta and data file for cbioportal to work on microbiome data?

That would be greatly appreciated if you can respond this post.

Harry

[Ramya Madupuri]

Hi Harry,

Sure, cBioPortal supports microbiome data using the generic assay format. You can refer to the file formats here and check out the example data and meta files as well as the case list files provided in the pull request.

Let us know if you have any further questions.

Thanks,

Ramya

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[Harry Sun]

Hi Ramya,

I appreciate your answer. Can you mention or give all data and meta files for the study. I read cbioportal's document that describes:

Generic assay data includes two types,"TREATMENT_RESPONSE" or "MUTATIONAL_SIGNATURE". But why did you use "MICROBIOME_SIGNATURE"? Can I name any type?  By cbioportal document, MUTATIONAL_SIGNATURE requires "contribution" data and other option matrix data as count,pvalue. My understanding is that your TCGA microbiome should be used as "contribution" data, is it correct?

My questions are:

1. What all data and meta did you use in the study except you link microbiome data and meta file?

2. In cbioportal.org, which study do you use microbiome data? If there is a study in cbioportal.org, I will get its data files and see its results.

Thank you,

Harry

[Ramya Madupuri]

Hi Harry,

The Treatment_Response and Mutational_Signature are two examples listed in the documentation. The generic assay format is flexible and holds non-genetic measurements per sample. You can name the data type based on the kind of data you are working with. In our case, we were using log-CPM values from microbiome expression data and labeled it MICROBIOME_SIGNATURE.

To answer your questions:
1. The only data and meta files used for microbiome are the ones I already shared. You can also check the pull request to see exactly what was added. 
2. We had added microbiome data to the TCGA PanCancer studies for a short time, but it was later retracted due to contamination concerns in the source data. There aren’t any studies with microbiome data at the moment.

You can use the data and meta file formats from the pull request as a reference to load your own data. Hope this helps!

Thanks,

Ramya

[Harry Sun]

Hi Ramya,

I am interested in your result as the below oncoprint.

For cbioportal, any query is done by genes. Do you have the other data file including genes associated with the microbiome signature?How does this data look like? If you used the mutation data, how did you do mutation data with microbiome signature? or how do you make microbiome data get the above oncoprint?

Sorry, bother you for so many questions .

Thanks a lot!

Harry

[Ramya Madupuri]

Hi Harry,

Microbiome data is measured at the genus/species level per sample, so a gene file is not required. The heatmap can be viewed by selecting Microbiome Signature from the Tracks dropdown and choosing species you are interested in (see the screenshot below for a similar example from another generic assay profile).

Let us know if you have any other questions.

Thanks,

Ramya

[Harry Sun]

Hi Ramya,

I loaded tcga microbiome data you linked into our local cbioportal, but I did not get oncoprint as you posted. Due to no gene data as mutation or copy number, I can't query by a gene set. I had to use the other studies including Microbiome data to get into the page queried result. I found tab Microbiome Signature by clicking tracks,  then I picked up a few tracks from Microbiome Signature and added them, but I didn't see any tracks in the oncoprint as you posted . Although your cbioportal.org does not have any example of Microbiome, you have some Mutational Signature's studies. I used your Mutational Signature, so that I didn't find any tracks added into oncoprint as the picture you posted. Why did I look for your picture? because it is Microbiome or Mutational Signature tracks on oncoprint we are looking for.

Hopefully you find my problems for me or if you show oncoprint for Mutational Signature's tracks in cbioportal.org

Thank you,

Harry

[Ramya Madupuri]

Hi Harry,

Just to confirm, you loaded the Microbiome Signature data, but when you selected a few tracks from the Microbiome Signature dropdown, no tracks were displayed. Is that correct? If possible, could you share a screenshot of what you are seeing?

Thanks,

Ramya