question about treatment response in CCLE dataset

[Di Benedetto, Carolina]

Hello,

We would like to study correlations between gene expression and treatment response using data from the Cancer Cell Line Encyclopedia (Broad 2019) on cBioPortal. For this, we use the "plots" tab, where we plot mRNA levels of our gene of interest versus treatment response for each compound, as IC50 or AUC. However, only 100 of 266 drugs are shown in the dropdown menu. As we want to analyze all of them, is there a way to display all of the compounds in the dropdown menu? 

Thank you,

Carolina Di Benedetto

[Tali Mazor]

Hi Carolina,

We only show 100 by default, but if you search for a drug it will appear -- so to access the drugs after those first 100, you'll need to search for them. If you're doing this for all drugs, you could also consider downloading the data (https://github.com/cBioPortal/datahub/tree/master/public/ccle_broad_2019) and automating the generation of these plots offline.

-Tali

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[Di Benedetto, Carolina]

I see, thank you very much for your quick reply.

Best,

Carolina

---

De: Tali Mazor <tma...@ds.dfci.harvard.edu>
Enviado: viernes, 17 de marzo de 2023 7:02
Para: Di Benedetto, Carolina <Carolina.D...@ucsf.edu>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>; Adrian Fu <adri...@berkeley.edu>
Asunto: Re: [cbioportal] question about treatment response in CCLE dataset

 

Hi Carolina, We only show 100 by default, but if you search for a drug it will appear -- so to access the drugs after those first 100, you'll need to search for them. If you're doing this for all drugs, you could also consider downloading

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