2008
DOI: 10.1074/mcp.m700574-mcp200
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GPS 2.0, a Tool to Predict Kinase-specific Phosphorylation Sites in Hierarchy

Abstract: Identification of protein phosphorylation sites with their cognate protein kinases (PKs) is a key step to delineate molecular dynamics and plasticity underlying a variety of cellular processes. Although nearly 10 kinase-specific prediction programs have been developed, numerous PKs have been casually classified into subgroups without a standard rule. For large scale predictions, the false positive rate has also never been addressed. In this work, we adopted a well established rule to classify PKs into a hierar… Show more

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Cited by 598 publications
(625 citation statements)
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References 39 publications
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“…To gain more insight into this process, we investigated pathways reported to affect TDP-43 localization because of their structural homology and the fact they are both mutated in ALS. In particular, staurosporine, a nonselective kinase inhibitor, has been reported to cause redistribution of TDP-43 from its nuclear localization to the cytoplasm (Zhang et al, 2007). In agreement with previous data, staurosporine treatment of human H4 neuroglioma cells for 3 h led to increased cytoplasmic levels of TDP-43 and smaller 35 and 25 kDa fragments that result from cleavage by Caspase-3 (Fig.…”
Section: Fus Is Phosphorylated and Translocates To The Cytoplasm Aftesupporting
confidence: 80%
“…To gain more insight into this process, we investigated pathways reported to affect TDP-43 localization because of their structural homology and the fact they are both mutated in ALS. In particular, staurosporine, a nonselective kinase inhibitor, has been reported to cause redistribution of TDP-43 from its nuclear localization to the cytoplasm (Zhang et al, 2007). In agreement with previous data, staurosporine treatment of human H4 neuroglioma cells for 3 h led to increased cytoplasmic levels of TDP-43 and smaller 35 and 25 kDa fragments that result from cleavage by Caspase-3 (Fig.…”
Section: Fus Is Phosphorylated and Translocates To The Cytoplasm Aftesupporting
confidence: 80%
“…Our results suggest that phosphorylation at serines 861/864 may serve as an obligate priming event. The GPS2.1 group-based prediction system (48) indicated that LGR5 contains a myriad of putative phosphorylation sites that include motifs for casein kinase1/2 and G protein receptor kinases (supplemental Table 1), which could affect receptor desensitization and signaling (28, 56 -58). Position 864 in particular is predicted to be a substrate of the G protein receptor kinase superfamily, and additional studies will be necessary to fully characterize the specific kinases involved.…”
Section: Discussionmentioning
confidence: 99%
“…34,35 We were able to predict a potential kinase group, family and/or subfamily for 30 out of 94 upregulated phosphosites (32%) and 33 out of 126 downregulated phosphosites (26%) (ESI, † Table S3). For the background set, Fig.…”
Section: -Fold Regulated Upon 007-am Stimulationmentioning
confidence: 99%