Inferring the Sign of Kinase-Substrate Interactions by Combining Quantitative Phosphoproteomics with a Literature-Based Mammalian Kinome Network

Abstract

Protein phosphorylation is a reversible post-translational modification commonly used by cell signaling networks to transmit information about the extracellular environment into intracellular organelles for the regulation of the activity and sorting of proteins within the cell. For this study we reconstructed a literature-based mammalian kinase-substrate network from several online resources. The interactions within this directed graph network connect kinases to their substrates, through specific phosphosites including kinasekinase regulatory interactions. However, the "signs" of links, activation or inhibition of the substrate upon phosphorylation, within this network are mostly unknown. Here we show how we can infer the "signs" indirectly using data from quantitative phosphoproteomics experiments applied to mammalian cells combined with the literature-based kinase-substrate network. Our inference method was able to predict the sign for 321 links and 153 phosphosites on 120 kinases, resulting in signed and directed subnetwork of mammalian kinase-kinase interactions. Such an approach can rapidly advance the reconstruction of cell signaling pathways and networks regulating mammalian cells.

Fig. 1

Illustration of the algorithm used to predict the sign of regulatory links that connect kinases and phosphatases by merging data from a literature-based kinase-substrate network with SILAC phosphoproteomics publications. K- kinase; P-phosphatase; S- substrate.

Fig. 2

Breakdown of identified phophosites reported in different SILAC phosphoproteomics publications. A) All identified sites that displayed either increase or decrease in phosphorylation levels under some experimental condition. B) Counts of sites identified by the SILAC phosphoproteomics that also have a known upstream kinase from the literature-based kinase-substrate network.

Fig. 3

The largest connected component of the kinase-kinase network created from all inferred signs/effects. Nodes represent kinases; green arrows represent activations; red diamond heads represent inhibitions.