kinaseSubstrateProfile: Kinase substrate profiling

In PYangLab/PhosR: A set of methods and tools for comprehensive analysis of phosphoproteomics data

Kinase substrate profiling

Description

This function generates substrate profiles for kinases that have one or more substrates quantified in the phosphoproteome data.

Usage

kinaseSubstrateProfile(substrate.list, mat)

Arguments

substrate.list	a list of kinases with each element containing an array of substrates.
mat	a matrix with rows correspond to phosphosites and columns correspond to samples.

Value

Kinase profile list.

Examples

data('phospho_L6_ratio_pe')
data('SPSs')
data('PhosphoSitePlus')

ppe <- phospho.L6.ratio.pe
sites = paste(sapply(GeneSymbol(ppe), function(x)x),";",
    sapply(Residue(ppe), function(x)x),
    sapply(Site(ppe), function(x)x),
    ";", sep = "")
grps = gsub("_.+", "", colnames(ppe))
design = model.matrix(~ grps - 1)
ctl = which(sites %in% SPSs)
ppe = RUVphospho(ppe, M = design, k = 3, ctl = ctl)

phosphoL6 = SummarizedExperiment::assay(ppe, "normalised")

# filter for up-regulated phosphosites
phosphoL6.mean <- meanAbundance(phosphoL6, grps = grps)
aov <- matANOVA(mat=phosphoL6, grps = grps)
idx <- (aov < 0.05) & (rowSums(phosphoL6.mean > 0.5) > 0)
phosphoL6.reg <- phosphoL6[idx, ,drop = FALSE]

L6.phos.std <- standardise(phosphoL6.reg)

ks.profile.list <- kinaseSubstrateProfile(PhosphoSite.mouse, L6.phos.std)

PYangLab/PhosR documentation built on Nov. 1, 2024, 1:47 p.m.