getPtmInfo {isobar} | R Documentation

## 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`.

### 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)

[Package isobar version 1.38.0 Index]