Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Filters applied. Clear all
. 2014 Mar 31;4:4524.
doi: 10.1038/srep04524.

PSEA: Kinase-specific Prediction and Analysis of Human Phosphorylation Substrates

Affiliations
Free PMC article

PSEA: Kinase-specific Prediction and Analysis of Human Phosphorylation Substrates

Sheng-Bao Suo et al. Sci Rep. .
Free PMC article

Abstract

Protein phosphorylation catalysed by kinases plays crucial regulatory roles in intracellular signal transduction. With the increasing number of kinase-specific phosphorylation sites and disease-related phosphorylation substrates that have been identified, the desire to explore the regulatory relationship between protein kinases and disease-related phosphorylation substrates is motivated. In this work, we analysed the kinases' characteristic of all disease-related phosphorylation substrates by using our developed Phosphorylation Set Enrichment Analysis (PSEA) method. We evaluated the efficiency of our method with independent test and concluded that our approach is reliable for identifying kinases responsible for phosphorylated substrates. In addition, we found that Mitogen-activated protein kinase (MAPK) and Glycogen synthase kinase (GSK) families are more associated with abnormal phosphorylation. It can be anticipated that our method might be helpful to identify the mechanism of phosphorylation and the relationship between kinase and phosphorylation related diseases. A user-friendly web interface is now freely available at http://bioinfo.ncu.edu.cn/PKPred_Home.aspx.

Figures

Figure 1
Figure 1. The ROC curve and the corresponding AUCs for phosphoserine prediction of different single kinases.
Figure 2
Figure 2. Comparison of our method with other existing methods on independent set for different kinase families.
(A), compared by accuracy (Acc); (B), compared by sensitivity (Sn); (C), compared by specificity (Sp); (D), compared by Matthews correlation coefficient (MCC).
Figure 3
Figure 3. The data statistics of predicted phosphoserine kinase family types for disease-related and normal phosphorylation substrates.
Significant differences (P-value) refer to the Two-sided category. Statistical significance was calculated with a Fisher exact test.
Figure 4
Figure 4. The relationship between specified kinases (MAPK3 and PLK1) and disease-related phosphorylation substrates (only displayed directly contacted interactions).
The nodes with green border line represent the specified kinases and the nodes with blue border line represent the diseased phosphorylation substrates. Bar plot represents the degrees of MAPK3 and PLK1.
Figure 5
Figure 5. The data statistics of pathway terms for disease-related and normal phosphorylation substrates.
Significant differences (P-value) refer to the Two-sided category. Statistical significance was calculated with a Fisher exact test.
Figure 6
Figure 6. Detailed processes of the PSEA method.

Similar articles

See all similar articles

Cited by 5 articles

References

    1. Wood C. D., Thornton T. M., Sabio G., Davis R. A. & Rincon M. Nuclear localization of p38 MAPK in response to DNA Damage. Int. J. Biol. Sci. 5, 428–437 (2009). - PMC - PubMed
    1. Uddin S. et al. Role of Stat5 in Type I interferon-signaling and transcriptional regulation. Biochem. Biophys. Res. Commun. 308, 325–330 (2003). - PubMed
    1. Zhang J. W. & Johnson G. V. W. Tau protein is hyperphosphorylated in a site-specific manner in apoptotic neuronal PC12 cells. J. Neurochem. 75, 2346–2357 (2000). - PubMed
    1. Kim S. H. & Lee C. E. Counter-regulation mechanism of IL-4 and IFN-alpha signal transduction through cytosolic retention of the pY-STAT6:pY-STAT2:p48 complex. Eur. J. Immunol. 41, 461–472 (2011). - PubMed
    1. Bu Y. H. et al. Insulin receptor substrate 1 regulates the cellular differentiation and the matrix metallopeptidase expression of preosteoblastic cells. J. Endocrinol. 206, 271–277 (2010). - PubMed

Publication types

MeSH terms

Substances

Feedback