Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data
Fig 1
The level of phosphorylation for each phosphorylation sites in the proteome are quantified in time-course by mass spectrometry. First, time-course profiles of phosphorylation sites are partitioned into clusters using a k-means clustering-based algorithm for a range of values for k. Next, the clustering result, for each k, is evaluated based on the correct clustering of known substrates of kinases, as annotated in the PhosphoSitePlus database [53], and an enrichment score is computed. The clustering with the highest enrichment score is reported as the optimal clustering along with kinases whose substrates are enriched within each cluster.