Survival comparison High vs low expression

[Rowyn Liebau]

Hello, 

I want to use the cbioportal site to compare patient survival curves between tumors displaying high expression and low expression of a gene. I can analyze groups comparing altered and unaltered samples, but the altered group is a mix of high and low expressing patients, likely obscuring any effects. Is there a way to set up separate high and low expression groups based on mRNA expression and a z score cutoff, as I can do for the oncoprint tract?

Thank you for your help,

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Rowyn Liebau

She/her 

PhD candidate Gautier Lab

Columbia University

[Tali Mazor]

Hi Rowyn,

There are two ways you can approach this. If you run a query, which sounds like the approach you've been taking, you can use OQL to generate separate tracks for high vs low expressing samples based on a z-score cutoff, eg

EGFR: EXP>1
EGFR: EXP<-1

You'll see this in OncoPrint as two distinct tracks. If you then click over to the Comparison tab, you have the option to deselect the 'Altered group' and 'Unaltered group' and instead select the groups corresponding to your query/OncoPrint tracks:

https://www.cbioportal.org/results/oncoprint?cancer_study_list=lgg_tcga_pan_can_atlas_2018&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Cgistic%2Crna_seq_v2_mrna_median_all_sample_Zscores&case_set_id=lgg_tcga_pan_can_atlas_2018_cnaseq&gene_list=EGFR%253A%2520EXP%253E1%250AEGFR%253A%2520EXP%253C-1&geneset_list=%20&tab_index=tab_visualize&Action=Submit

Another option is to use study view to define groups, which is demonstrated in more detail in this video: https://www.youtube.com/watch?v=HTiKUXk0j0s

-Tali

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