Benchmarking substrate-based kinase activity inference using phosphoproteomic data.

ABSTRACT:

Motivation

Phosphoproteomic experiments are increasingly used to study the changes in signaling occurring across different conditions. It has been proposed that changes in phosphorylation of kinase target sites can be used to infer when a kinase activity is under regulation. However, these approaches have not yet been benchmarked due to a lack of appropriate benchmarking strategies.

Results

We used curated phosphoproteomic experiments and a gold standard dataset containing a total of 184 kinase-condition pairs where regulation is expected to occur to benchmark and compare different kinase activity inference strategies: Z-test, Kolmogorov Smirnov test, Wilcoxon rank sum test, gene set enrichment analysis (GSEA), and a multiple linear regression model. We also tested weighted

SUBMITTER: Hernandez-Armenta C 

PROVIDER: S-EPMC5870625 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature