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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

Improved confidence in S-palmitoylation protein hits.A: Analysis of the 1372 human hits contained in 8 palmitoyl proteomes: 672 S-palmitoylation hits are present in at least 2 human palmitoyl proteomes or are annotated as “high confident hits” (HC). 204 are only found in at least 2 human palmitoyl proteomes, 136 are only classified as HC and 332 S-palmitoylation hits are both found in more than one palmitoyl-proteome and classified as HC. Out of the 672 hits, 345 are identified with 2 independent techniques. 63 out of the 672 S-palmitoylation hits have been validated in targeted studies, while 24 out of 700 hits only found in 1 human palmitoyl proteome have been validated.B: Analysis of the 1747 mouse hits contained in 6 palmitoyl proteomes as described inA.C: Analysis of the 2541 human orthologous hits contained in 19 palmitoyl proteomes as described inA.D: Number of the S-palmitoylation hits by the occurrence of palmitoyl-proteomes in which they have been identified.
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f2: Improved confidence in S-palmitoylation protein hits.A: Analysis of the 1372 human hits contained in 8 palmitoyl proteomes: 672 S-palmitoylation hits are present in at least 2 human palmitoyl proteomes or are annotated as “high confident hits” (HC). 204 are only found in at least 2 human palmitoyl proteomes, 136 are only classified as HC and 332 S-palmitoylation hits are both found in more than one palmitoyl-proteome and classified as HC. Out of the 672 hits, 345 are identified with 2 independent techniques. 63 out of the 672 S-palmitoylation hits have been validated in targeted studies, while 24 out of 700 hits only found in 1 human palmitoyl proteome have been validated.B: Analysis of the 1747 mouse hits contained in 6 palmitoyl proteomes as described inA.C: Analysis of the 2541 human orthologous hits contained in 19 palmitoyl proteomes as described inA.D: Number of the S-palmitoylation hits by the occurrence of palmitoyl-proteomes in which they have been identified.

Mentions: SwissPalm-mediated improvement of confidence. The information generated by independent palmitoyl-proteome studies was used to build a filter system that increases the hit confidence. First we annotated the proteins that are defined as high confidence by the authors of the studies (468 for human and 347 for mouse) (Figure 2A andFigure 2B,Supplementary table S1A andSupplementary table S1B). Second, we assume that the likelihood of a protein to be a true positive increases with its presence in multiple independent palmitoyl-proteomes. It is however important to keep in mind that even if proteins were isolated using the ABE/Acyl-RAC method of labeling followed by click chemistry, all proteins that contain a thioester bond, not related to S-palmitoylation, will be recovered and thus constitute false positives.


SwissPalm: Protein Palmitoylation database.

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

Improved confidence in S-palmitoylation protein hits.A: Analysis of the 1372 human hits contained in 8 palmitoyl proteomes: 672 S-palmitoylation hits are present in at least 2 human palmitoyl proteomes or are annotated as “high confident hits” (HC). 204 are only found in at least 2 human palmitoyl proteomes, 136 are only classified as HC and 332 S-palmitoylation hits are both found in more than one palmitoyl-proteome and classified as HC. Out of the 672 hits, 345 are identified with 2 independent techniques. 63 out of the 672 S-palmitoylation hits have been validated in targeted studies, while 24 out of 700 hits only found in 1 human palmitoyl proteome have been validated.B: Analysis of the 1747 mouse hits contained in 6 palmitoyl proteomes as described inA.C: Analysis of the 2541 human orthologous hits contained in 19 palmitoyl proteomes as described inA.D: Number of the S-palmitoylation hits by the occurrence of palmitoyl-proteomes in which they have been identified.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: Improved confidence in S-palmitoylation protein hits.A: Analysis of the 1372 human hits contained in 8 palmitoyl proteomes: 672 S-palmitoylation hits are present in at least 2 human palmitoyl proteomes or are annotated as “high confident hits” (HC). 204 are only found in at least 2 human palmitoyl proteomes, 136 are only classified as HC and 332 S-palmitoylation hits are both found in more than one palmitoyl-proteome and classified as HC. Out of the 672 hits, 345 are identified with 2 independent techniques. 63 out of the 672 S-palmitoylation hits have been validated in targeted studies, while 24 out of 700 hits only found in 1 human palmitoyl proteome have been validated.B: Analysis of the 1747 mouse hits contained in 6 palmitoyl proteomes as described inA.C: Analysis of the 2541 human orthologous hits contained in 19 palmitoyl proteomes as described inA.D: Number of the S-palmitoylation hits by the occurrence of palmitoyl-proteomes in which they have been identified.
Mentions: SwissPalm-mediated improvement of confidence. The information generated by independent palmitoyl-proteome studies was used to build a filter system that increases the hit confidence. First we annotated the proteins that are defined as high confidence by the authors of the studies (468 for human and 347 for mouse) (Figure 2A andFigure 2B,Supplementary table S1A andSupplementary table S1B). Second, we assume that the likelihood of a protein to be a true positive increases with its presence in multiple independent palmitoyl-proteomes. It is however important to keep in mind that even if proteins were isolated using the ABE/Acyl-RAC method of labeling followed by click chemistry, all proteins that contain a thioester bond, not related to S-palmitoylation, will be recovered and thus constitute false positives.

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