RNAi (Achilles+DRIVE+Marcotte, DEMETER2) meaning

Q&A
1

Hello,

I want to identify HER2 positive breast cancer cell lines. I downloaded the relevant file from DepMap and created column for ERBB2 (NGL, c-ERB-2, HER-2, c-ERB2, CD340, NEU, MLN-19, p185(erbB2), HER2) using cell line selector. Additionally, I am curious about the meaning of RNAi (Achilles+DRIVE+Marcotte, DEMETER2) and how to interpret these data values. What does a data value of 0 or less mean? Can I consider cell lines with values of 0 or less as HER2 positive cell lines?

I’ll wait for your response.

Thank you.
Jaeeun

2

It sounds like you downloaded D2_combined_gene_dep_scores.csv correct?

These values are “gene effect scores” and a short description of the scale can be seen in the gene effect tooltip on the portal:

image

However, you’re also asking about “HER2 positive” which sounds like you’re referring to the diagnostic marker for amplified levels of HER2 expression, which is measuring a something very different then a dependency on HER2. (Although, I can imagine they may go hand-in-hand)

Thanks,
Phil