Fig. 3: Comparison of kinase activity inference methods.
From: A computational tool to infer enzyme activity using post-translational modification profiling data
a Heatmap depicting the z-score normalized kinase activities between two conditions, P31/Fuj, and Kasumi-1 cell lines, as determined by JUMPsem without motif-assisted search, JUMPsem with motif-assisted search, IKAP, and KSEA. Colors correspond to activity levels: red indicates high kinase activity, and blue indicates low kinase activity. Three clusters (Cluster 1, Cluster 2, and Cluster 3) are annotated to the right of each heatmap, indicating groupings of kinases based on activity patterns. The waterfall plot on the right is the result from KSEA, which we applied to compare with IKAP and our JUMPsem. b Volcano plot illustrating the variation in kinase activity between P31/Fuj and Kasumi-1 cell lines, as inferred by JUMPsem with motif search. The x-axis denotes the log2 fold change, where positive values suggest increased activity in P31/Fuj relative to Kasumi-1, and negative values denote decreased activity. The y-axis corresponds to the negative logarithm (base 10) of the p-value, with higher values signifying more substantial statistical significance. c Bar chart representing pathways enriched in protein kinases with heightened activity in P31/Fuj compared to Kasumi-1 inferred from IKAP. The x-axis indicates the positions of the pathway members in the ranked list of proteins, while the y-axis lists the pathways. The values in parenthesis indicate the enrichment score, quantifying the overrepresentation for each pathway. The order of the protein position is ranked by the fold change score of kinase activity. d Bar chart detailing pathways enriched in protein kinases with heightened activity in P31/Fuj relative to Kasumi-1 inferred from JUMPsem with motif assisted, using the same axes format as in (c).
