getPtmInfo {isobar} | R Documentation |
Get PTM site information for idenfied proteins from public databases.
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")
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 |
wildcard to replace with Uniprot protein AC in |
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.
data.frame with (at least) the columns: isoform_ac, description, evidence, position
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.
Florian P. Breitwieser
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.
## 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)