KinomeXplorer

[…] used to reveal the enriched annotations for biological function and cellular component. GO subgroups that were significantly enriched with p-values below 0.05 were reported.NetworKIN 3.0 (as part of KinomeXplorer) was used to generate kinase-substrate networks. Predictions scoring ≥5 were selected. Predicted kinase-substrate interaction networks were visualized using Cytoscape 3.4.0. Cellular com […]

[…] y Analysis (IPA) (Qiagen, Redwood City, CA, USA), in particular by generating networks of protein–protein relationships. As background, the set of all proteins detected in the experiment was used.The KinomeXplorer toolset (; ; ) was applied to predict likely kinases causing the observed phosphorylation changes. Two programs were used, NetPhorest, the atlas of consensus phosphorylation site sequenc […]

[…] he HR between CR2 and CR3, and the C-terminus (Figure ). This suggests that these areas reside in less-ordered states allowing easy access for kinases and phosphatases. Using bioinformatic tools like KinomeXplorer, Scansite or PhosphoNET, we list which kinases could be implicated in these phosphorylation events (). […]

[…] ate the minimum centroid distance (minimum distance between two cluster centers produced by c-means clustering) (Schwammle & Jensen, ). Prediction of kinase–substrate relationships was achieved using KinomeXplorer with default thresholding criteria (Horn et al, ) (http://networkin.info/). Gene ontology enrichment analyses were performed against whole S. cerevisiae proteome as background using DAVI […]

[…] sifier for predicting protein phosphorylation sites [–, ]. Another method Musite is considered for large scale predictions of both non-kinase and kinase-specific phosphorylation sites []. RegPhos and KinomeXplorer are two latest tools, aimed to explore kinase signaling networks [, ]. Recently in 2014, Suo et al. have proposed a method PSEA for predicting kinase specific phosphorylation sites as we […]