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>.

Version: 0.0.1
Depends: R (≥ 3.3.0)
Published: 2017-12-22
Author: Peter Liao [aut, cre]
Maintainer: Peter Liao <pll21 at case.edu>
License: MIT + file LICENSE
NeedsCompilation: no
Materials: README
CRAN checks: pKSEA results

Downloads:

Reference manual: pKSEA.pdf
Package source: pKSEA_0.0.1.tar.gz
Windows binaries: r-devel: pKSEA_0.0.1.zip, r-release: pKSEA_0.0.1.zip, r-oldrel: pKSEA_0.0.1.zip
OS X El Capitan binaries: r-release: pKSEA_0.0.1.tgz
OS X Mavericks binaries: r-oldrel: pKSEA_0.0.1.tgz

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