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. 2008 Jan;36(Database issue):D240-4.
doi: 10.1093/nar/gkm772. Epub 2007 Oct 25.

Phospho.ELM: a database of phosphorylation sites--update 2008

Francesca Diella  1 , Cathryn M Gould, Claudia Chica, Allegra Via, Toby J Gibson
Affiliations

Phospho.ELM: a database of phosphorylation sites--update 2008

Francesca Diella et al. Nucleic Acids Res. 2008 Jan.

Abstract

Phospho.ELM is a manually curated database of eukaryotic phosphorylation sites. The resource includes data collected from published literature as well as high-throughput data sets. The current release of Phospho.ELM (version 7.0, July 2007) contains 4078 phospho-protein sequences covering 12 025 phospho-serine, 2362 phospho-threonine and 2083 phospho-tyrosine sites. The entries provide information about the phosphorylated proteins and the exact position of known phosphorylated instances, the kinases responsible for the modification (where known) and links to bibliographic references. The database entries have hyperlinks to easily access further information from UniProt, PubMed, SMART, ELM, MSD as well as links to the protein interaction databases MINT and STRING. A new BLAST search tool, complementary to retrieval by keyword and UniProt accession number, allows users to submit a protein query (by sequence or UniProt accession) to search against the curated data set of phosphorylated peptides. Phospho.ELM is available on line at: http://phospho.elm.eu.org.

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Figures

Figure 1.
Figure 1.
The plot shows the growth of the Phospho.ELM data set beginning with version 1.0 in December 2003 (panel A). The exponential growth of the phosphorylation instances from Version 5.0 is mainly due to incorporation of the high-throughput data sets. The overlapping of the instances derived from low-throughput (LTP) and high-throughput (HTP) experiments is also shown (panel B).
Figure 2.
Figure 2.
Output example of a PhosphoBLAST Search using as query the Danio rerio Aurora A kinase sequence. The summary graphic shows the phospho-hits on the query sequence and features from SMART. Details about the matches are shown below in the results table. Clicking on the ‘subject name’ the users can retrieve additional information about the matched Phospho.ELM phosphorylated sites, including the flanking sequence, the PubMed reference, the kinase responsible for the phosphorylation (where known) and links to additional information for the substrate and other relevant databases.
See this image and copyright information in PMC

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