Is it possible to bulk-download gene expression + methylation data for a specific copy number loss on TCGA?

Question

[Pratik]

Hello Biostars community,

There's three filters I guess that would need to be applied.

Is it possible to bulk-download

• gene expression data
• methylation array data

for the same patient (for multiple patients) for a:

• specific copy number loss

on TCGA-COAD?

Say for example APC copy number loss.

Or if you have a better option like another database or something, what would you use for this kind-of query?

Respectfully, Pratik

[Zhenyu Zhang]

Isn't this the standard use case of the GDC: you upload a APC cnv loss case set, and download corresponding files?

if you don't have the case set

1. you can learn how to use gdc api to query for cnv loss
2. if you don't know how to use api, you can go to APC gene page, and find COAD in the plot and make the case set
3. or you wait for GDC v2 release

Answer 1

[GenoMax]

How about: https://www.cbioportal.org/results/oncoprint?cancer_study_list=coad_caseccc_2015%2Ccoad_cptac_2019%2Ccoad_silu_2022%2Ccoadread_dfci_2016%2Ccoadread_genentech%2Ccoadread_tcga%2Ccoadread_tcga_pub%2Ccoadread_tcga_pan_can_atlas_2018%2Ccoadread_mskcc%2Ccoadread_mskresistance_2022&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Cgistic%2Ccna&case_set_id=all&gene_list=APC&geneset_list=%20&tab_index=tab_visualize&Action=Submit

I don't see methylation array data

[Pratik]

Thank you GenoMax !

This is good for me. I found the IDs of the patients or samples at least with APC gene mutations so this helps alot.

On the cBioPortal you linked, I went to the Downloads tab, got the IDs from the unaltered samples download, and searched the IDs on gdc.cancer.gov - TCGA website to find the methylation data and counts for RNAseq. Perfecto!

and I just learned how to download them in bulk through the gdc portal.

If you add your comment as an answer I will accept : )