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

Diella F, Gould CM, Chica C, Via A, Gibson TJ - Nucleic Acids Res. (2007)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.

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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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).
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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).

Mentions: The content and the format of Phospho.ELM have been previously described in Diella et al. (13). While the general format of the database has remained essentially unchanged, some additions have been implemented to improve the data retrieval and presentation. The updated version also contains a much larger number of phosphorylation sites (see Figure 1), a new search tool based on sequence comparison and a Web Services interface.Figure 1.


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

Diella F, Gould CM, Chica C, Via A, Gibson TJ - Nucleic Acids Res. (2007)

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).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238828&req=5

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).
Mentions: The content and the format of Phospho.ELM have been previously described in Diella et al. (13). While the general format of the database has remained essentially unchanged, some additions have been implemented to improve the data retrieval and presentation. The updated version also contains a much larger number of phosphorylation sites (see Figure 1), a new search tool based on sequence comparison and a Web Services interface.Figure 1.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.

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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