Clarifying data format, continuous copy number

Michael Rightmire

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Jul 14, 2021, 10:30:51 AM7/14/21

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Hello All,

I'm looking at the cBioPortal documentation at https://docs.cbioportal.org/5.1-data-loading/data-loading/file-formats#continuous-copy-number-data

The meta file description discusses using either ...

datatype: CONTINUOUS
stable_id: linear_CNA
...or...
datatype: LOG2-VALUE
stable_id: log2CNA

It then discusses that you can use the data from the GISTIC generated file <prefix>_all_data_by_genes.txt I'm not super familiar with GISTIC output, but I assume (if I use the GISTIC file) I should use log2 datatype and ID?

datatype: LOG2-VALUE
stable_id: log2CNA

Thanks!

Michael Rightmire

Bioinformatics and Omics Data Analytics (B240)

Omics Software Architect

German Cancer Research Center (DKFZ)

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

phone: +49 176 7131 8758

fax: +49 6221 42-3563

M.Rightmire@dkfz-heidelberg.de

www.dkfz.de

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Ino de Bruijn

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Jul 14, 2021, 12:44:58 PM7/14/21

to Michael Rightmire, cBioPortal for Cancer Genomics Discussion Group, Ritika Kundra, Y

Hi Michael,

Thanks for reaching out!

I believe you should indeed use:

datatype: LOG2-VALUE
stable_id: log2CNA

CC'ing some more members of our team to confirm

Best wishes,

Ino

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Michael Rightmire

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Jul 14, 2021, 4:55:18 PM7/14/21

to Ino de Bruijn, cBioPortal for Cancer Genomics Discussion Group, Ritika Kundra, Y

Hi Ino,

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Michael Rightmire

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Jul 23, 2021, 7:15:07 AM7/23/21

to Ino de Bruijn, cBioPortal for Cancer Genomics Discussion Group, Ritika Kundra, Y, gistic...@broadinstitute.org

Hi Ino,

Upon further examination, it seems it's not the negative values in the all_data_by_genes.txt file, it that occasionally the Entrez_Gene_Id column ends up with a negative integer, instead of a valid Gene ID. It seems to happen only with data lines that have Hugo symbols for RNA in the format hsa-mir-xxxx. Any idea why this is happening? Do those negative integers hold any meaning, or can they just be replaced with N/a? Hugo_Symbol : hsa-mir-4320 Entrez_Gene_Id : -948 Cytoband : 18q21.1 <ID1>.tumor021-01 : 0.180 <ID2>.tumor011-01 : -0.013 <ID3>.tumor001-01 : 0.122 <ID2>.tumor011-01 : -0.008 ================== Hugo_Symbol : hsa-mir-122 Entrez_Gene_Id : -1013 Cytoband : 18q21.31 <ID1>.tumor021-01 : 0.335 <ID2>.tumor011-01 : -0.013 <ID3>.tumor001-01 : 0.122 <ID2>.tumor011-01 : -0.015
Thanks!
Mike

Ino de Bruijn

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Aug 2, 2021, 4:15:00 PM8/2/21

to Michael Rightmire, cBioPortal for Cancer Genomics Discussion Group, Ritika Kundra, Y, gistic...@broadinstitute.org

Hi Michael,

Apologies for the delay in replying. The negative integers can be safely ignored. They aren't really valid genes but we've used them internally to represent non-gene entities such as e.g. expression of miRNA.