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SwissPalm: Protein Palmitoylation database.

Blanc M, David F, Abrami L, Migliozzi D, Armand F, Bürgi J, van der Goot FG - F1000Res (2015)

Bottom Line: Systems analysis of the palmitoyl-proteome screens indicate that 10% or more of the human proteome is susceptible to S-palmitoylation.Moreover, ontology and pathway analyses of the human palmitoyl-proteome reveal that key biological functions involve this reversible lipid modification.Through the compilation of data and continuous updates, SwissPalm will provide a powerful tool to unravel the global importance of protein S-palmitoylation.

View Article: PubMed Central - PubMed

Affiliation: Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland.

ABSTRACT
Protein S-palmitoylation is a reversible post-translational modification that regulates many key biological processes, although the full extent and functions of protein S-palmitoylation remain largely unexplored. Recent developments of new chemical methods have allowed the establishment of palmitoyl-proteomes of a variety of cell lines and tissues from different species.  As the amount of information generated by these high-throughput studies is increasing, the field requires centralization and comparison of this information. Here we present SwissPalm ( http://swisspalm.epfl.ch), our open, comprehensive, manually curated resource to study protein S-palmitoylation. It currently encompasses more than 5000 S-palmitoylated protein hits from seven species, and contains more than 500 specific sites of S-palmitoylation. SwissPalm also provides curated information and filters that increase the confidence in true positive hits, and integrates predictions of S-palmitoylated cysteine scores, orthologs and isoform multiple alignments. Systems analysis of the palmitoyl-proteome screens indicate that 10% or more of the human proteome is susceptible to S-palmitoylation. Moreover, ontology and pathway analyses of the human palmitoyl-proteome reveal that key biological functions involve this reversible lipid modification. Comparative analysis finally shows a strong crosstalk between S-palmitoylation and other post-translational modifications. Through the compilation of data and continuous updates, SwissPalm will provide a powerful tool to unravel the global importance of protein S-palmitoylation.

No MeSH data available.


Related in: MedlinePlus

Search and result page.A: SwissPalm search page: Example of query for “calnexin” shows that it has been found in palmitoyl-proteomes from several species: human (7 out of 8 screens), mouse (6 out of 6), rat (1 out of 1) andArabidopsis thaliana (1 out of 1). For human, mouse and rat calnexin was classified as a high confident hit and for human and mouse identified by two independent techniques (metabolic labeling and chemical capture). Finally, calnexin S-palmitoylation was also subject to targeted studies and 2 cysteine residues (502 and 503 in human calnexin) were identified.B: Results Page from human calnexin display summary boxes containing the main information related to S-palmitoylation: number of occurrences in palmitoyl-proteome screens and targeted studies, sites information, cysteine prediction.
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f3: Search and result page.A: SwissPalm search page: Example of query for “calnexin” shows that it has been found in palmitoyl-proteomes from several species: human (7 out of 8 screens), mouse (6 out of 6), rat (1 out of 1) andArabidopsis thaliana (1 out of 1). For human, mouse and rat calnexin was classified as a high confident hit and for human and mouse identified by two independent techniques (metabolic labeling and chemical capture). Finally, calnexin S-palmitoylation was also subject to targeted studies and 2 cysteine residues (502 and 503 in human calnexin) were identified.B: Results Page from human calnexin display summary boxes containing the main information related to S-palmitoylation: number of occurrences in palmitoyl-proteome screens and targeted studies, sites information, cysteine prediction.

Mentions: Search page. The web-based search tool is accessible from any page of the SwissPalm website:www.swisspalm.epfl.ch and produces as output a list of proteins with a direct link to detailed information for each protein (Figure 3A). Protein searches are initiated by submitting a protein name, gene name or Uniprot_ID in the query section and protein IDs that match the string search will be returned in the results sections. Protein searches can be restricted to specific criteria. These include: ‘species’, ‘presence in palmitoyl-proteome screens’, ‘predicted to be S-palmitoylated’ or ‘obtained from a third party application/tool’ (e.g. from a complex query on the UniProt website). Search can also be restricted to the “reviewed” annotated UniProtKB/SwissProt proteins. Batch searches are possible by submitting a list of identifiers in a tab/csv file (in the first column). An advanced search tool is available to help the user choosing among identifiers recognized by the search engine. Also, it presents controlled vocabularies that can be used to perform complex queries within the database (Motif Search, GO term and Subcellular localization).


SwissPalm: Protein Palmitoylation database.

Blanc M, David F, Abrami L, Migliozzi D, Armand F, Bürgi J, van der Goot FG - F1000Res (2015)

Search and result page.A: SwissPalm search page: Example of query for “calnexin” shows that it has been found in palmitoyl-proteomes from several species: human (7 out of 8 screens), mouse (6 out of 6), rat (1 out of 1) andArabidopsis thaliana (1 out of 1). For human, mouse and rat calnexin was classified as a high confident hit and for human and mouse identified by two independent techniques (metabolic labeling and chemical capture). Finally, calnexin S-palmitoylation was also subject to targeted studies and 2 cysteine residues (502 and 503 in human calnexin) were identified.B: Results Page from human calnexin display summary boxes containing the main information related to S-palmitoylation: number of occurrences in palmitoyl-proteome screens and targeted studies, sites information, cysteine prediction.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4544385&req=5

f3: Search and result page.A: SwissPalm search page: Example of query for “calnexin” shows that it has been found in palmitoyl-proteomes from several species: human (7 out of 8 screens), mouse (6 out of 6), rat (1 out of 1) andArabidopsis thaliana (1 out of 1). For human, mouse and rat calnexin was classified as a high confident hit and for human and mouse identified by two independent techniques (metabolic labeling and chemical capture). Finally, calnexin S-palmitoylation was also subject to targeted studies and 2 cysteine residues (502 and 503 in human calnexin) were identified.B: Results Page from human calnexin display summary boxes containing the main information related to S-palmitoylation: number of occurrences in palmitoyl-proteome screens and targeted studies, sites information, cysteine prediction.
Mentions: Search page. The web-based search tool is accessible from any page of the SwissPalm website:www.swisspalm.epfl.ch and produces as output a list of proteins with a direct link to detailed information for each protein (Figure 3A). Protein searches are initiated by submitting a protein name, gene name or Uniprot_ID in the query section and protein IDs that match the string search will be returned in the results sections. Protein searches can be restricted to specific criteria. These include: ‘species’, ‘presence in palmitoyl-proteome screens’, ‘predicted to be S-palmitoylated’ or ‘obtained from a third party application/tool’ (e.g. from a complex query on the UniProt website). Search can also be restricted to the “reviewed” annotated UniProtKB/SwissProt proteins. Batch searches are possible by submitting a list of identifiers in a tab/csv file (in the first column). An advanced search tool is available to help the user choosing among identifiers recognized by the search engine. Also, it presents controlled vocabularies that can be used to perform complex queries within the database (Motif Search, GO term and Subcellular localization).

Bottom Line: Systems analysis of the palmitoyl-proteome screens indicate that 10% or more of the human proteome is susceptible to S-palmitoylation.Moreover, ontology and pathway analyses of the human palmitoyl-proteome reveal that key biological functions involve this reversible lipid modification.Through the compilation of data and continuous updates, SwissPalm will provide a powerful tool to unravel the global importance of protein S-palmitoylation.

View Article: PubMed Central - PubMed

Affiliation: Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland.

ABSTRACT
Protein S-palmitoylation is a reversible post-translational modification that regulates many key biological processes, although the full extent and functions of protein S-palmitoylation remain largely unexplored. Recent developments of new chemical methods have allowed the establishment of palmitoyl-proteomes of a variety of cell lines and tissues from different species.  As the amount of information generated by these high-throughput studies is increasing, the field requires centralization and comparison of this information. Here we present SwissPalm ( http://swisspalm.epfl.ch), our open, comprehensive, manually curated resource to study protein S-palmitoylation. It currently encompasses more than 5000 S-palmitoylated protein hits from seven species, and contains more than 500 specific sites of S-palmitoylation. SwissPalm also provides curated information and filters that increase the confidence in true positive hits, and integrates predictions of S-palmitoylated cysteine scores, orthologs and isoform multiple alignments. Systems analysis of the palmitoyl-proteome screens indicate that 10% or more of the human proteome is susceptible to S-palmitoylation. Moreover, ontology and pathway analyses of the human palmitoyl-proteome reveal that key biological functions involve this reversible lipid modification. Comparative analysis finally shows a strong crosstalk between S-palmitoylation and other post-translational modifications. Through the compilation of data and continuous updates, SwissPalm will provide a powerful tool to unravel the global importance of protein S-palmitoylation.

No MeSH data available.


Related in: MedlinePlus