Kinase—Substrate Enrichment Analysis (KSEA) of the phosphoproteomics differential analysis results using kinase sets from PhosphoSitePlus.
PHOSPHO_KSEAA named list of 3 data.frame objects. Similar to what is in
GO_FGSEA.
See PSP_KINASE_SUBSTRATE for details on the kinase
sets.
Rat phosphorylation sites in PHOSPHO_DA were mapped to their
human orthologs and multiply-phosphorylated sites were split and aggregated
to the single-site level by taking the arithmetic mean of the
-log\(_{10}\)(p-value) signed by the log\(_2\) fold-change. FGSEA was
then performed with fgsea2 by
grouping substrates according to their kinases and treating these kinase
groups as gene sets. Only those kinases with at least 3 substrates were
tested for enrichment.
Hornbeck, P. V., Zhang, B., Murray, B., Kornhauser, J. M., Latham, V., & Skrzypek, E. (2015). PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic acids research, 43(Database issue), D512–D520. https://doi.org/10.1093/nar/gku1267