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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

Palmitoyl-proteomes integrated in SwissPalm.A: Database content: Primary data on S-palmitoylation of proteins are extracted from MS large scale experiments on different species. Curated data on S-palmitoylation are obtained from the literature and input together with the MS information in the same data structure. In order to perform complex query related to S-palmitoylation, we have integrated in the database various external sources like orthology databases (Ortho_DB and OMA), UniProt features and subcellular localization information and Interpro domains. We ran also programs to have additional data, like multiple alignments of orthologous proteins or protein isoforms, and results from existing S-palmitoylation site predictors (CSS-Palm 4.0 and PalmPred). Web interface: The web interface presents the knowledge on S-palmitoylation in protein-centric pages. These pages are accessible through queries on a search engine. Some tools to analyse S-palmitoylation datasets are available online, like the orthologs comparison tool, aiming to perform cross-species S-palmitoylation comparison.B: 19 palmitoyl-proteomes from 7 species and various cell types and tissues were selected from published literature and integrated to SwissPalm. In total the dataset includes 5199 proteins.
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f1: Palmitoyl-proteomes integrated in SwissPalm.A: Database content: Primary data on S-palmitoylation of proteins are extracted from MS large scale experiments on different species. Curated data on S-palmitoylation are obtained from the literature and input together with the MS information in the same data structure. In order to perform complex query related to S-palmitoylation, we have integrated in the database various external sources like orthology databases (Ortho_DB and OMA), UniProt features and subcellular localization information and Interpro domains. We ran also programs to have additional data, like multiple alignments of orthologous proteins or protein isoforms, and results from existing S-palmitoylation site predictors (CSS-Palm 4.0 and PalmPred). Web interface: The web interface presents the knowledge on S-palmitoylation in protein-centric pages. These pages are accessible through queries on a search engine. Some tools to analyse S-palmitoylation datasets are available online, like the orthologs comparison tool, aiming to perform cross-species S-palmitoylation comparison.B: 19 palmitoyl-proteomes from 7 species and various cell types and tissues were selected from published literature and integrated to SwissPalm. In total the dataset includes 5199 proteins.

Mentions: Palmitoyl-proteomes. 19 palmitoyl-proteome screens using ABE-, Acyl-RAC- or click chemistry-based studies were selected from published literature (for details and references see:http://swisspalm.epfl.ch/studies?large_scale=1). They cover seven species and ten palmitoyl proteomes performed with ABE, 2 with Acyl-RAC and 7 with click chemistry (Figure 1A).


SwissPalm: Protein Palmitoylation database.

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

Palmitoyl-proteomes integrated in SwissPalm.A: Database content: Primary data on S-palmitoylation of proteins are extracted from MS large scale experiments on different species. Curated data on S-palmitoylation are obtained from the literature and input together with the MS information in the same data structure. In order to perform complex query related to S-palmitoylation, we have integrated in the database various external sources like orthology databases (Ortho_DB and OMA), UniProt features and subcellular localization information and Interpro domains. We ran also programs to have additional data, like multiple alignments of orthologous proteins or protein isoforms, and results from existing S-palmitoylation site predictors (CSS-Palm 4.0 and PalmPred). Web interface: The web interface presents the knowledge on S-palmitoylation in protein-centric pages. These pages are accessible through queries on a search engine. Some tools to analyse S-palmitoylation datasets are available online, like the orthologs comparison tool, aiming to perform cross-species S-palmitoylation comparison.B: 19 palmitoyl-proteomes from 7 species and various cell types and tissues were selected from published literature and integrated to SwissPalm. In total the dataset includes 5199 proteins.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Palmitoyl-proteomes integrated in SwissPalm.A: Database content: Primary data on S-palmitoylation of proteins are extracted from MS large scale experiments on different species. Curated data on S-palmitoylation are obtained from the literature and input together with the MS information in the same data structure. In order to perform complex query related to S-palmitoylation, we have integrated in the database various external sources like orthology databases (Ortho_DB and OMA), UniProt features and subcellular localization information and Interpro domains. We ran also programs to have additional data, like multiple alignments of orthologous proteins or protein isoforms, and results from existing S-palmitoylation site predictors (CSS-Palm 4.0 and PalmPred). Web interface: The web interface presents the knowledge on S-palmitoylation in protein-centric pages. These pages are accessible through queries on a search engine. Some tools to analyse S-palmitoylation datasets are available online, like the orthologs comparison tool, aiming to perform cross-species S-palmitoylation comparison.B: 19 palmitoyl-proteomes from 7 species and various cell types and tissues were selected from published literature and integrated to SwissPalm. In total the dataset includes 5199 proteins.
Mentions: Palmitoyl-proteomes. 19 palmitoyl-proteome screens using ABE-, Acyl-RAC- or click chemistry-based studies were selected from published literature (for details and references see:http://swisspalm.epfl.ch/studies?large_scale=1). They cover seven species and ten palmitoyl proteomes performed with ABE, 2 with Acyl-RAC and 7 with click chemistry (Figure 1A).

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