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, 38 (Database issue), D828-34

PhosPhAt: The Arabidopsis Thaliana Phosphorylation Site Database. An Update

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PhosPhAt: The Arabidopsis Thaliana Phosphorylation Site Database. An Update

Pawel Durek et al. Nucleic Acids Res.

Abstract

The PhosPhAt database of Arabidopsis phosphorylation sites was initially launched in August 2007. Since then, along with 10-fold increase in database entries, functionality of PhosPhAt (phosphat.mpimp-golm.mpg.de) has been considerably upgraded and re-designed. PhosPhAt is now more of a web application with the inclusion of advanced search functions allowing combinatorial searches by Boolean terms. The results output now includes interactive visualization of annotated fragmentation spectra and the ability to export spectra and peptide sequences as text files for use in other applications. We have also implemented dynamic links to other web resources thus augmenting PhosPhAt-specific information with external protein-related data. For experimental phosphorylation sites with information about dynamic behavior in response to external stimuli, we display simple time-resolved diagrams. We have included predictions for pT and pY sites and updated pS predictions. Access to prediction algorithm now allows 'on-the-fly' prediction of phosphorylation of any user-uploaded protein sequence. Protein Pfam domain structures are now mapped onto the protein sequence display next to experimental and predicted phosphorylation sites. Finally, we have implemented functional annotation of proteins using MAPMAN ontology. These new developments make the PhosPhAt resource a useful and powerful tool for the scientific community as a whole beyond the plant sciences.

Figures

Figure 1.
Figure 1.
Screenshots of new PhosPhAt web interface. (A) Entry screen with advanced search, (B) result window, (C) peptide summary and (D) protein summary.
Figure 2.
Figure 2.
Percentage of phosphoproteins and phosphorylation sites from PhosPhAt corresponding to the number of independent experimental set-ups. Numbers are based on independent Medline entries.
Figure 3.
Figure 3.
Values of the AUC for prediction of phosphorylation sites based on an independent test set, which are varying by the minimal number of supporting experimental reports (identification). The AUC is plotted against the number of identifications.

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