Citations

Phosphomatics draws upon a number of open-source and freely-available resources. A brief description of how each is incorporated into Phosphomatics is provided below. In addition to Phosphomatics, please consider citing the relevant publications below in your own work.

Resource Title Use in Phosphomatics
PhosphoSitePlus PhosphoSitePlus, 2014: mutations, PTMs and recalibrations Core resource for the construction of substrate-kinase interaction networks
SIGNOR 2.0 SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update Core resource for the construction of substrate-kinase interaction networks
KSEA App The KSEA App: a web-based tool for kinase activity inference from quantitative phosphoproteomics The scripts underpinning KSEA are utilised in Phosphomatics to perform kinase enrichment analysis
UniProt UniProt: a worldwide hub of protein knowledge Retrieval of protein sequence, PTM and processing information
iTextMine iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature Literature text-mining to identify publications relevant to selected substrate-kinase interactions
DrugBank DrugBank 5.0: a major update to the DrugBank database for 2018. Ligands interaction with upstream kinases
IUPHAR/BPS Guide to PHARMACOLOGY The IUPHAR/BPS Guide to PHARMACOLOGY in 2020: extending immunopharmacology content and introducing the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY. Ligands interaction with upstream kinases
g:Profiler g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update) Pathway and GO-term enrichment analysis for selected substrate groups
Logomaker Logomaker: beautiful sequence logos in Python Construction of sequence logo plots for substrates of selected kinases