OmicsCNGene.csv lacks some of the key oncogene data

Q&A
1

Hi, I am trying to analyze the OmicsCNGene.csv file to get the copy number gains and loss information for some of the key oncogenes we are interested in (like MYC, CDKN2A etc.). These gene information’s are missing in the above CSV file. Could someone guide me as to where I can find the copy number ratio data for all of the genes? Also, for gain I am planning to use ratio above 2 as positive for amplification. What would be a good ratio value to consider for homozygous deletions?

Thank you in advance!

2

Hi,

Thanks for reaching out. I can’t seem to reproduce this error: I can see both MYC (4609) and CDKN2A (1029) as columns in the OmicsCNGene.csv file from the latest release.

Were you reading the file using excel? If so, I’d strongly recommend loading these files programmatically, since sometimes excel cannot load all the columns correctly if the file is really big.

Let me know if this resolves the issue,
Simone

3

Thanks for your suggestion. Yes, I have been reading the file through excel. I will try to read the file programmatically and see if it fixes the problem.