Obtaining matched transcriptomic and CNA data

[Richard Louis Anderson]

Dear CBio team

I am trying to generate data comparing CNV/A data to transcriptomic data, to see how copy number alterations affect transcripts at a gene & tissue-/cancer-specific level. Ideally, I would end up with 

CNA -> either gene by patient ID or genomic position by patient ID

Transcripts -> gene by patient ID

I am able to select studies that have both CNA and transcript information but I am having trouble getting the detailed information. Is this possible, if so how, if not could you get a list of studies that have both these sources of information (so I can [try to] manually retrieve this information)?

Just to say, I am master's student so I don't want or need patient confidential data.

Kind regards

Richard Anderson

[Priti Kumari]

Hi Richard,

You can go to the dataset page: https://www.cbioportal.org/datasets and use the columns CNA and RNA-Seq to identify studies that have both CNA and transcriptomics data. Once you select the study, you can query for genes of interest and then select the 'Plots' tab to compare CNA and expression data. 

Here is an example: https://www.cbioportal.org/results/plots?cancer_study_list=laml_tcga_pan_can_atlas_2018&tab_index=tab_visualize&case_set_id=laml_tcga_pan_can_atlas_2018_all&Action=Submit&gene_list=TP53%250ANRAS%250AKRAS

Hope this helps.

Thanks,

Priti

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[Richard Louis Anderson]

HI Priti

Yes, that helps. Thank you

Richard