in CCLE_expression.csv，there are TBCE (6905).1 and TBCE (6905) / PINX1(54984.1) and PINX1(54984) .which one is right?
Yes, this occurred in the 20Q4 release and we’re planning to fix it in the 21Q4 release. You can see the explanation in Duplicate genes in the RNA seq data in 20Q4
Thanks! So, which one should I keep? And I also found that there are more than 18789 gene in Mutation.csv, and their IDs are all 0, what do these mean?
The issue with duplicate genes will be fixed in the upcoming release (21q1). Meanwhile, you can add the TPM values for the genes with duplicate names.
As of the mutations, could you clarify what IDs you’re referring to?
These are oncotator annotations. Unfortunately the tool is somewhat old and possibly is replacing missing IDs to 0 if it does not find a mapping. Hopefully we will be able to update this at some point if time permits.