I am currently conducting research using the DepMap portal, particularly interested in the “Oncogenic Alterations” displayed on cell line pages, such as ACH-000328. I am seeking clarification on the methodology used to identify these specific oncogenic gene alterations.
In an effort to replicate this aspect of the data, I selected genes from the Mutations dataset where the ‘Likely LOF’ (Loss of Function) column is marked as TRUE. However, I’ve noticed that the list of genes I compiled greatly exceeds the number presented on the website’s page.
Could someone kindly provide insight into the additional conditions or filters that might be applied to determine the genes listed under “Oncogenic Alterations” on the DepMap portal? Understanding the precise criteria or methodology used in this process would be immensely helpful for my research.
Thank you in advance for your time and help.