DbPAF: An integrative database of protein phosphorylation in animals and fungi

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Ullah, Shahid ^a   Lin, Shaofeng ^a   Xu, Yang ^a   Deng, Wankun ^a   Ma, Lili ^a   Zhang, Ying ^a   Liu, Zexian ^a   Xue, Yu ^a  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN; PROTEIN;

AMINO ACID SEQUENCE; ANIMAL; CHEMISTRY; METABOLISM; PHOSPHORYLATION; PROTEIN DATABASE; SYSTEM ANALYSIS;

AMINO ACID SEQUENCE; ANIMALS; DATABASES, PROTEIN; FUNGAL PROTEINS; PHOSPHORYLATION; PROTEINS; SYSTEMS INTEGRATION;

EID: 84961601422     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep23534     Document Type: Article

References (48)

1. Linding, R. et al. Systematic discovery of in vivo phosphorylation networks. Cell 129, 1415-1426 (2007).
2. Jin, J. & Pawson, T. Modular evolution of phosphorylation-based signalling systems. Philos Trans R Soc Lond B Biol Sci 367, 2540-2555 (2012).
3. Seet, B. T., Dikic, I., Zhou, M. M. & Pawson, T. Reading protein modifications with interaction domains. Nat Rev Mol Cell Biol 7, 473-483 (2006).
4. Pan, Z. et al. dbPSP: a curated database for protein phosphorylation sites in prokaryotes. Database (Oxford) 2015, bav031 (2015).
5. Cheng, H. et al. dbPPT: a comprehensive database of protein phosphorylation in plants. Database (Oxford) 2014, bau121 (2014).
6. Li, L. et al. The human phosphotyrosine signaling network: evolution and hotspots of hijacking in cancer. Genome Res 22, 1222-1230 (2012).
7. Ubersax, J. A. & Ferrell, J. E. Jr. Mechanisms of specificity in protein phosphorylation. Nat Rev Mol Cell Biol 8, 530-541 (2007).
8. Faller, W. J. et al. mTORC1-mediated translational elongation limits intestinal tumour initiation and growth. Nature 517, 497-500 (2015).
9. Martin, I. et al. Ribosomal protein s15 phosphorylation mediates LRRK2 neurodegeneration in Parkinson's disease. Cell 157, 472-485 (2014).
10. Lahiry, P., Torkamani, A., Schork, N. J. & Hegele, R. A. Kinase mutations in human disease: interpreting genotype-phenotype relationships. Nat Rev Genet 11, 60-74 (2010).
11. Humphrey, S. J., Azimifar, S. B. & Mann, M. High-throughput phosphoproteomics reveals in vivo insulin signaling dynamics. Nat Biotechnol 33, 990-995 (2015).
12. Zanivan, S. et al. In Vivo SILAC-Based Proteomics Reveals Phosphoproteome Changes during Mouse Skin Carcinogenesis. Cell Rep 3, 552-566 (2013).
13. Lundby, A. et al. Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues. Nat Commun 3, 876 (2012).
14. Horn, H. et al. KinomeXplorer: an integrated platform for kinome biology studies. Nat Methods 11, 603-604 (2014).
15. Miller, M. L. et al. Linear motif atlas for phosphorylation-dependent signaling. Sci Signal 1, ra2 (2008).
16. Xue, Y. et al. GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy. Mol Cell Proteomics 7, 1598-1608 (2008).
17. Qi, L. et al. Systematic analysis of the phosphoproteome and kinase-substrate networks in the mouse testis. Mol Cell Proteomics 13, 3626-3638 (2014).
18. Beltrao, P. et al. Systematic functional prioritization of protein posttranslational modifications. Cell 150, 413-425 (2012).
19. Wagih, O., Reimand, J. & Bader, G. D. MIMP: predicting the impact of mutations on kinase-substrate phosphorylation. Nat Methods 12, 531-533 (2015).
20. Wang, Y. et al. Reconfiguring phosphorylation signaling by genetic polymorphisms affects cancer susceptibility. J Mol Cell Biol 7, 187-202 (2015).
21. Blom, N., Kreegipuu, A. & Brunak, S. PhosphoBase: a database of phosphorylation sites. Nucleic Acids Res 26, 382-386 (1998).
22. Diella, F., Gould, C. M., Chica, C., Via, A. & Gibson, T. J. Phospho.ELM: a database of phosphorylation sites-update 2008. Nucleic Acids Res 36, D240-244 (2008).
23. Diella, F. et al. Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinformatics 5, 79 (2004).
24. Lee, T. Y. et al. dbPTM: an information repository of protein post-translational modification. Nucleic Acids Res 34, D622-627 (2006).
25. Olsen, J. V. et al. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127, 635-648 (2006).
26. Gnad, F., Gunawardena, J. & Mann, M. PHOSIDA 2011: the posttranslational modification database. Nucleic Acids Res 39, D253-260 (2011).
27. Huang, K. Y. et al. dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins. Nucleic Acids Res (2015).
28. Hornbeck, P. V. et al. PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res 43, D512-520 (2015).
29. Hornbeck, P. V., Chabra, I., Kornhauser, J. M., Skrzypek, E. & Zhang, B. PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics 4, 1551-1561 (2004).
30. Bodenmiller, B. et al. PhosphoPep-A database of protein phosphorylation sites in model organisms. Nat Biotechnol 26, 1339-1340 (2008).
31. Bodenmiller, B. et al. PhosphoPep-A phosphoproteome resource for systems biology research in Drosophila Kc167 cells. Mol Syst Biol 3, 139 (2007).
32. Sadowski, I. et al. The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update. Database (Oxford) 2013, bat026 (2013).
33. Stark, C. et al. PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae. Database (Oxford) 2010, bap026 (2010).
34. Li, J. et al. SysPTM 2.0: an updated systematic resource for post-translational modification. Database (Oxford) 2014, bau025 (2014).
35. Li, H. et al. SysPTM: a systematic resource for proteomic research on post-translational modifications. Mol Cell Proteomics 8, 1839-1849 (2009).
36. Goel, R., Harsha, H. C., Pandey, A. & Prasad, T. S. Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. Mol Biosyst 8, 453-463 (2012).
37. UniProt: a hub for protein information. Nucleic Acids Res 43, D204-212 (2015).
38. Boratyn, G. M. et al. BLAST: a more efficient report with usability improvements. Nucleic Acids Res 41, W29-33 (2013).
39. Hunter, T. Tyrosine phosphorylation: thirty years and counting. Curr Opin Cell Biol 21, 140-146 (2009).
40. Wang, Y. et al. EKPD: a hierarchical database of eukaryotic protein kinases and protein phosphatases. Nucleic Acids Res 42, D496-502 (2014).
41. Lindberg, R. A., Quinn, A. M. & Hunter, T. Dual-specificity protein kinases: will any hydroxyl do? Trends Biochem Sci 17, 114-119 (1992).
42. Iakoucheva, L. M. et al. The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res 32, 1037-1049 (2004).
43. Minguez, P. et al. Deciphering a global network of functionally associated post-translational modifications. Mol Syst Biol 8, 599 (2012).
44. van Wijk, K. J., Friso, G., Walther, D. & Schulze, W. X. Meta-Analysis of Arabidopsis thaliana Phospho-Proteomics Data Reveals Compartmentalization of Phosphorylation Motifs. Plant Cell 26, 2367-2389 (2014).
45. Schwartz, D. & Gygi, S. P. An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets. Nat Biotechnol 23, 1391-1398 (2005).
46. Sonnhammer, E. L. & Ostlund, G. InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic. Nucleic Acids Res 43, D234-239 (2015).
47. Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7, 539 (2011).
48. Letunic, I. & Bork, P. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 39, W475-478 (2011).