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 |
Documentation:
Downloads:
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