getPtmInfo: Get PTM site information for idenfied proteins from public...

In isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

Description

Get PTM site information for idenfied proteins from public databases.

Usage

  getPtmInfoFromPhosphoSitePlus(protein.group, file.name = NULL, modif = "PHOS", 
                                psp.url = "http://www.phosphosite.org/downloads/", 
                                mapping = c(PHOS = "Phosphorylation_site_dataset.gz", 
                                            ACET = "Acetylation_site_dataset.gz", 
                                            METH = "Methylation_site_dataset.gz", 
                                            SUMO = "Sumoylation_site_dataset.gz", 
                                            UBI = "Ubiquitination_site_dataset.gz"))

  getPtmInfoFromNextprot(protein.group, nextprot.url = "http://www.nextprot.org/rest/entry/NX_XXX/ptm?format=json",
                         url.wildcard = "XXX")

Arguments

protein.group	ProteinGroup object.
file.name	File name to save downloaded data, defaults to the original file name (see mapping).
modif	Selects dataset to download (see mapping).
psp.url	PhosphoSitePlus main URL for datasets.
mapping	Names of PhosphoSitePlus modification datasets, mapped by modif name.
nextprot.url	URL for fetching Nextprot results. url.wildcard will be replaced by the Uniprot Protein AC.
url.wildcard	wildcard to replace with Uniprot protein AC in nextprot.url.

Details

PhosphoSitePlus datasets are downloaded and written to the working directory with its original name (see mapping) unless a file with that name exists, which is then parsed into a data.frame of suitable format.

Value

data.frame with (at least) the columns: isoform_ac, description, evidence, position

Note

PhosphoSitePlus is licensed under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License and is freely available for non-commercial purpose, see http://www.phosphosite.org/staticDownloads.do.

neXtProt is licensed under the Creative Commons Attribution-NoDerivs License, see: http://creativecommons.org/licenses/by-nd/3.0.

Please read the conditions and use the data only if you agree.

Author(s)

Florian P. Breitwieser

References

PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M. Nucleic Acids Res. 2012 Jan;40(Database issue):D261-70. Epub 2011 Dec 1.

neXtProt: a knowledge platform for human proteins. Lane L, Argoud-Puy G, Britan A, Cusin I, Duek PD, Evalet O, Gateau A, Gaudet P, Gleizes A, Masselot A, Zwahlen C, Bairoch A. Nucleic Acids Res. 2012 Jan;40(Database issue):D76-83. Epub 2011 Dec 1.

Examples

## Not run: 
  data(ib_phospho)
  ptm.info.np <- getPtmInfoFromNextprot(proteinGroup(ib_phospho))
  ptm.info.np <- ptm.info.np[grep("Phospho",ptm.info.np$modification.name),]
  ptm.info.psp <- getPtmInfoFromPhosphoSitePlus(proteinGroup(ib_phospho),modif="PHOS")

  str(ptm.info.np)
  str(ptm.info.psp)

  
## End(Not run)

isobar documentation built on Nov. 8, 2020, 7:48 p.m.