Bommi2008

Kinase requirements in human cells: III. Altered kinase requirements in VHL-/- cancer cells detected in a pilot synthetic lethal screen.

• Bommi-Reddy A, Proc Natl Acad Sci U S A. 105(43):16484-9

The paper describes the use of two cell types: 786-O (Table S4) and RCC4 (Table S5). Each of these cells has a loss of function mutation in the tumor suppressor gene VHL. The defects in the other gene were induced with a lentiviral vector that produced a shRNA. The final results are in Tables S4 and S5. The authors require a differential viability above 35% for the 786-O cells or a differential viability above 20% for the RCC4 cells. We have copied that values from the supplemental tables (which were PDF files) into a TSV file called data/bommi-reddy-2008.tsv. For the output file, we demand that at least one shRNA was above threshold, and just report the best outcome per gene. The authors showed experimentally that two genes, IRR and HER4, actually are not SL, so we remove these by hand