In WubingZhang/rMAUPS: Model-Based Analysis of Ubiquitin-Proteome System Based Protein Degradation.

knitr::opts_chunk$set(echo = TRUE)

This vignette assumes that you have already properly installed rMAUPS.

Searching protein sequence

First, load the rMAUPS package.

library(rMAUPS)

Next, read in protein sequences from uniprot.

uniprot_path <- system.file("extdata", "human_uniprot_seq.txt", package = "rMAUPS")
uniprot <- read.delim(uniprot_path, sep='\t')
head(uniprot)

Next, search the protein sequences for lysine residues ("K").

lysine_pos <- searchProtSeq(head(uniprot), 'K')
head(lysine_pos)

Note, for the sake of a quick example, the above command only searched against the top few protein sequences. Additionally, although not used here, the searchProtSeq function can also handle searching for sequences using regular expression.

Viewing protein structure

First, we'll view all of the lysine residues for KRAS.

# get hits for P01116
id <- 'P01116'
start <- lysine_pos[lysine_pos['UniprotId']==id, 'start']
end <- lysine_pos[lysine_pos['UniprotId']==id, 'end']

# view on protein structure
browseProtStructure(id, start, end)

Next, we'll compare those to the lysines with reported ubiquitination sites.

# Here, we manually create a dataframe for the KRAS ubiqutination sites.
# In the realisitic scenario, you should load the "Ubiquitination_site_dataset" file
# from PhosphositePlus DB using the readPSPUbiquitin function. You'll need to download
# it your self due to copy protection.
id <- 'P01116'
ub <- data.frame(gene='KRAS', ID=id, position=c(117, 128, 147))

# get ub sites for P01116
start <- ub[ub['ID']==id, 'position']
end <- ub[ub['ID']==id, 'position']

# view on protein structure
browseProtStructure(id, start, end)

Session info

sessionInfo()

WubingZhang/rMAUPS documentation built on March 21, 2022, 8:48 p.m.