isobar (version 1.18.0)

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

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.

Value

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

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.

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)