In this study, we present a flexible framework to assess different combinations of computational algorithms and kinase-substrate libraries for the inference of kinase activities. For the benchmark, we use a set of kinase perturbation experiments to evaluate which combination is able to recapitulate the perturbed kinases from the phosphoproteomics data.
If you want to test your own method try out our package benchmarKIN and check out the documentation.
We have included the following kinase-substrate libraries:
- PhosphoSitePlus
- PTMsigDB
- Omnipath
- Gold Standard set of GPS 6.0
- iKiP-db
- NetworKIN
Additionally have tested the combination with predicted targets including the Kinase Library and Phosformer.
We have included the following methods for the comparison:
- fgsea
- KARP
- Kologomorov-Smirnov
- linear model (RoKAI, decoupler)
- mean
- normalised mean
- median
- multivarite linear model
- PC1
- PTM-SEA
- sum
- upper quantile
- viper
- Wilcox
- z-score (KSEA, RoKAI)
Mueller-Dott, Sophia, Eric J. Jaehnig, Khoi Pham Munchic, Wen Jiang, Tomer M. Yaron-Barir, Sara R. Savage, Martin Garrido-Rodriguez, et al. 2024. “Comprehensive Evaluation of Phosphoproteomic-Based Kinase Activity Inference.” bioRxiv. https://doi.org/10.1101/2024.06.27.601117.