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 |
| Sugiyama et. al. 2019 | Large-scale Discovery of Substrates of the Human Kinome | Secondary 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 |
| LIMMA | limma powers differential expression analyses for RNA-sequencing and microarray studies | Statistical analysis of phosphorylation site quantitative data |
| PDB | The Protein Data Bank | Protein structural data displayed on Substrate Explorer page |