KSEAdb

<p>A data table containing all known kinase-substrate links known in PhosphoSitePlus.</p>

datasets

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>.

Peter Liao

pKSEA

Prediction-Based Kinase-Substrate Enrichment Analysis

KSEAdb function

<p>An object of class <code>data.frame</code> with 240749 rows and 6 columns.</p>

KSEAdb: KSEAdb

Description

Usage

Arguments

Format

References