Effect of a monogenetic change in a cancer cell line use case

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INKA, an integrative data analysis pipeline for phosphoproteomic inference of active kinases Effect of a monogenetic change in a cancer cell line use case. Comparison of U87 glioblastoma cells (“wild‐type”) with isogenic U87‐EGFRvIII cells overexpressing a constitutively active EGFR variant (“mutant”) grown under baseline conditions. Effect of drug treatment in a cancer cell line use case. Comparison of U87‐EGFRvIII cells at baseline with U87‐EGFRvIII cells treated with 10 μM erlotinib for 2 h shows a clearly reduced INKA score for EGFR. Effect of drug treatment in a patient with hypopharyngeal cancer. Tumor biopsies were taken both before and after 2 weeks of erlotinib treatment. Same as panel (C), but for a patient with pancreatic cancer. Time‐dependent effect of radiomimetic treatment in a cancer cell line use case. MS intensity‐based INKA analysis of TiO2‐captured phosphoproteomes from G361 melanoma cells at different time points following treatment with the DNA damage‐inducing drug neocarzinostatin (NCS) in the absence or presence of ATM inhibitor KU55933 (ATM). Plotted is the INKA score for ATM, exhibiting a time‐dependent increase, which is not observed with ATM blocking. Full INKA score bar graphs are shown in Appendix Fig S10. As these data were generated using an LTQ‐FT mass spectrometer that is less sensitive than current orbitrap‐based instruments, spectral count data did not work well, and MS intensity data were analyzed instead. Same as panel (E), but plotting of the INKA score for PRKDC/DNA‐PK, which exhibits similar behavior. Data information: Raw data for panels (A and B) are from van der Mijn et al (). Raw data for panels (E and F) are from Bensimon et al () and averaged for replicate treatment conditions. IF THIS IMAGE HAS BEEN PROVIDED BY OR IS OWNED BY A THIRD PARTY, AS INDICATED IN THE CAPTION LINE, THEN FURTHER PERMISSION MAY BE NEEDED BEFORE ANY FURTHER USE. PLEASE CONTACT WILEY'S PERMISSIONS DEPARTMENT ON PERMISSIONS@WILEY.COM OR USE THE RIGHTSLINK SERVICE BY CLICKING ON THE 'REQUEST PERMISSIONS' LINK ACCOMPANYING THIS ARTICLE. WILEY OR AUTHOR OWNED IMAGES MAY BE USED FOR NON-COMMERCIAL PURPOSES, SUBJECT TO PROPER CITATION OF THE ARTICLE, AUTHOR, AND PUBLISHER. Mol Syst Biol, Volume: 15, Issue: 4, First published: 12 April 2019, DOI: (10.15252/msb.20188250)