PHOSIDA: Difference between revisions
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Revision as of 13:26, 18 March 2008
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| Link/URL: | |
|---|---|
| What: |
Phosida - Phosphorylation Site Database |
| Who: |
Florian Gnad and Matthias Mann |
| Updates: |
Genome Annotation Section |
| Upcoming events: |
Inclusion of additional phosphoproteomes of various organisms |
| Web Services: | |
| edit table | |
See Help:Database_table for how to add or edit information in this section of EcoliWiki.
About PHOSIDA
Add general information here
PHOSIDA, the phosphorylation site database, integrates thousands of high-confidence in-vivo phosphosites identified by mass spectrometry-based proteomics in various species. It includes phosphoproteomes of organisms, which cover the entire phylogenetic tree representatively, ranging from bacteria such as Escherichia coli and Bacillus subtilis to eukaryotes such as yeast and human. It contains 81 phosphorylation sites on 79 E.coli proteins, for example.
E.coli results are described in Macek and Gnad et al.[1].
Content
PHOSIDA contains phosphoproteomes of the following prokaryotes:
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Escherichia coli (79 phosphoproteins, 81 phosphosites) |
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Bacillus subtilis (78 phosphoproteins, 78 phosphosites) |
| edit table |
Using PHOSIDA
Browsing
The web user is able to search for any protein of interest within a specified organism. In the case of human, it is possible to search via IPI accession number, Swissprot identifier, gene symbol, protein name, peptide sequence, protein sequence or any substring that matches with the description of a given protein, for example.
Searching
For each protein, the user is presented with general features such as isoelectric point (pI), molecular weight, sequence, and description at the protein level in addition to corresponding GO accession numbers, which are directly hyperlinked to the detailed description of the annotation at the Gene Ontology website. In addition, a hyperlink to the Reactome database is provided, if the specified protein is annotated in Reactome (www.reactome.org).
Furthermore, annotated protein features such as active sites, binding sites, domains, and signal sequences are derived from the Swissprot database and illustrated for eukaryotic phosphoproteins, when clicking the ‘motifs/domains’ button. In the case of human, protein assignments were based on the IPI database, which is cross-referenced with the Swissprot database by PHOSIDA. Entries of both databases that correspond to the same proteins were aligned to derive the exact positions of these protein features. Already annotated phosphosites derived from Swissprot are transferred to the IPI sequences in the same way and listed when clicking the ‘sites (other sources)’ button. The aligned regions can be visualized via ‘check alignment’ buttons. Furthermore, corresponding literature is also provided.
Moreover, all phosphorylated sites that have been identified in our laboratory are displayed on the left panel. This presentment allows to check immediately whether phosphorylation sites occur within known domains or signaling sequence regions. Additionally, it becomes instantly clear whether a known biologically functional site such as binding sites is phosphorylated. In such cases, one can link the phosphorylation event to its functional impact. If the localization probability is lower than 0.995, it is enclosed in round brackets. When users click on any of the displayed phosphosites, the surrounding sequence and matching kinase motifs are shown.
Often, several phosphopeptides covering the same phosphosite are measured by mass spectrometry. These peptides are also listed along with their localization probabilities, Mascot scores, and MSQuant/PTM scores for each instance. In many cases, for example, the growth factor treatment, PHOSIDA contains quantitative and time-resolved data for the relative abundance of each phosphopeptide. These data are listed separately for peptides as a function of their sequences, degrees of phosphorylation, and further categories, such as experimental design or fraction. When moving the mouse over the ‘occurences’ button, protein entries sharing the same phosphopeptide of interest are listed along with the number of unique peptides that have been measured in one experimental assay. Each peptide is color coded according to the protein assignment: if the peptide sequence is marked in green, the selected protein has the maximum number of peptides in comparison to all other proteins that contain the same peptide. If the protein assignment is ambiguous because of another protein with the same number of identified peptides, the peptide is highlighted in blue. Red indicates that other proteins exceed the number of detected peptides in comparison to the selected phosphoprotein. Each feature of PHOSIDA is explained in the help menu, which is accessible via the ‘background’ menu or via clicking on the ‘question mark’ button at the page of interest.
The evolutionary section of PHOSIDA displays the results of the homology searches using an approximate phylogeny of all investigated species. Taxonomic divisions are displayed on-screen when the cursor is pointed at the phylogenetic tree. If the selected phosphoprotein is not homologous to any protein of a certain organism, that organism is highlighted in red. If the similarity between the sequence of the phosphoprotein and its homologous protein was the significantly best one in both directions, the given organism is highlighted in green. A higher similarity between the sequence of the homologous protein and another protein of the organism of the selected phosphoprotein suggests paralogy, which is indicated in blue. The full global alignment between the given phosphoprotein and the orthologous protein of a specific organism is shown, when the web user clicks on the organism button.
Usage examples
Add links to additional pages describing success stories here.
Technology
Web Services/API
The underlying database of PHOSIDA is based on mySQL. In addition, we used C#/ASP.NET to generate the dynamic web application.
Discussion
References
External Links
PHOSIDA (Phosphorylation Site Database): http://www.phosida.com
MAPU (Max-Planck Unified Proteome Database): http://www.mapuproteome.com