pll21/pKSEA: Prediction-Based Kinase-Substrate Enrichment Analysis

A tool for inferring kinase activity changes from phosphoproteomics data. 'pKSEA' uses kinase-substrate prediction scores to weight observed changes in phosphopeptide abundance to calculate a phosphopeptide-level contribution score, then sums up these contribution scores by kinase to obtain a phosphoproteome-level kinase activity change score (KAC score). 'pKSEA' then assesses the significance of changes in predicted substrate abundances for each kinase using permutation testing. This results in a permutation score (pKSEA significance score) reflecting the likelihood of a similarly high or low KAC from random chance, which can then be interpreted in an analogous manner to an empirically calculated p-value. 'pKSEA' contains default databases of kinase-substrate predictions from 'NetworKIN' (NetworKINPred_db) <http://networkin.info> Horn, et. al (2014) <doi:10.1038/nmeth.2968> and of known kinase-substrate links from 'PhosphoSitePlus' (KSEAdb) <https://www.phosphosite.org/> Hornbeck PV, et. al (2015) <doi:10.1093/nar/gku1267>.

Getting started

Package details

MaintainerPeter Liao <[email protected]>
LicenseMIT + file LICENSE
Version0.0.1
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("remotes")
remotes::install_github("pll21/pKSEA")
pll21/pKSEA documentation built on May 27, 2019, 8:46 a.m.