SwissPalm: Protein Palmitoylation database [v1; ref status: indexed, http://f1000r.es/5co]
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...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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F1000 Research Ltd
2015-07-01
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| Series: | F1000Research |
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| Online Access: | http://f1000research.com/articles/4-261/v1 |
| _version_ | 1818119510319693824 |
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| author | Mathieu Blanc Fabrice David Laurence Abrami Daniel Migliozzi Florence Armand Jérôme Bürgi Françoise Gisou van der Goot |
| author_facet | Mathieu Blanc Fabrice David Laurence Abrami Daniel Migliozzi Florence Armand Jérôme Bürgi Françoise Gisou van der Goot |
| author_sort | Mathieu Blanc |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-11T05:11:21Z |
| format | Article |
| id | doaj.art-ba72c86b733644dab5e49197ff1b0a56 |
| institution | Directory Open Access Journal |
| issn | 2046-1402 |
| language | English |
| last_indexed | 2024-12-11T05:11:21Z |
| publishDate | 2015-07-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | F1000Research |
| spelling | doaj.art-ba72c86b733644dab5e49197ff1b0a562022-12-22T01:19:56ZengF1000 Research LtdF1000Research2046-14022015-07-01410.12688/f1000research.6464.16936SwissPalm: Protein Palmitoylation database [v1; ref status: indexed, http://f1000r.es/5co]Mathieu Blanc0Fabrice David1Laurence Abrami2Daniel Migliozzi3Florence Armand4Jérôme Bürgi5Françoise Gisou van der Goot6Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, SwitzerlandBioinformatics and biostatistics Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, SwitzerlandGlobal Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, SwitzerlandGlobal Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, SwitzerlandProteomic Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, SwitzerlandGlobal Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, SwitzerlandGlobal Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, SwitzerlandProtein 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.http://f1000research.com/articles/4-261/v1Cell SignalingData SharingMembranes & Sorting |
| spellingShingle | Mathieu Blanc Fabrice David Laurence Abrami Daniel Migliozzi Florence Armand Jérôme Bürgi Françoise Gisou van der Goot SwissPalm: Protein Palmitoylation database [v1; ref status: indexed, http://f1000r.es/5co] F1000Research Cell Signaling Data Sharing Membranes & Sorting |
| title | SwissPalm: Protein Palmitoylation database [v1; ref status: indexed, http://f1000r.es/5co] |
| title_full | SwissPalm: Protein Palmitoylation database [v1; ref status: indexed, http://f1000r.es/5co] |
| title_fullStr | SwissPalm: Protein Palmitoylation database [v1; ref status: indexed, http://f1000r.es/5co] |
| title_full_unstemmed | SwissPalm: Protein Palmitoylation database [v1; ref status: indexed, http://f1000r.es/5co] |
| title_short | SwissPalm: Protein Palmitoylation database [v1; ref status: indexed, http://f1000r.es/5co] |
| title_sort | swisspalm protein palmitoylation database v1 ref status indexed http f1000r es 5co |
| topic | Cell Signaling Data Sharing Membranes & Sorting |
| url | http://f1000research.com/articles/4-261/v1 |
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