Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data
Fig 5
Optimal clustering and analysis of hES cell phosphoproteomics data.
CLUE's estimation of number of clusters. The number of clusters evaluated ranges from 2 to 20 and the optimal number of clusters, as estimated by CLUE, is highlighted in red. Visual representation of temporal profiles of phosphorylation sites within each cluster. Membership scores of all phosphorylation sites within a cluster is used to create color gradient from green to red correspond to lower to higher clustering confidence. Size: number of phosphorylation sites that have membership in that cluster. Bar plot showing kinases whose substrates are enriched within each cluster (p-value < 0.05; Fisher’s exact test). Principal component analysis of the temporal profile of phosphorylation sites within clusters 3, 6, and 7. Known substrates of p70S6K and ERK kinases are highlighted as x and *, respectively. Motif enrichment analysis. Phosphorylation sites from each cluster are scored against the PSSMs of p70S6K and ERK1, respectively. The cluster with the highest motif enrichment scores (median) are highlighted in yellow.