Phosphomatics helps you make sense of your high-throughput phosphoproteomics data. Our aim is to help you connect the phosphorylation sties that you observe in your mass spectrometry experiments to known upstream kinases. This provides a greater understanding of the regulatory signalling networks operating in your systems.
How to use Phosphomatics
Phosphomatics takes in a list of phosphorylated proteins. The minimal analysis requires only 3 data fields for each phoshpoprotein. These are: 1) The Uniprot identifier of the protein, 2) the residue phosphorylated, and 3) the type of residue (serine, threonine or tyrosine).
How does Phosphomatics work?
Phosphomatics combines data from a number of sources to provide residue level information about phosphorylation events.
|Signor 2.0||An excellend database of substrate-kinase interactions manually curated from literature sources. Signor is developed and maintained by Prof. Gianni Cesareni and co-workers and the relevant publication is here|
|iTextMine||For a specific relationship between a given kinase and substrate pair, 'iTextMine' is utilised to search the literature and shotrlist publicatiosns that may describe this interaction. here|
|BioGrid||Protein-level interaction data and evidence is retrieved from BioGrid. This does not necessarily relate to phosphorylation events, or to phosphorylation at any given site, but may nonetheless be useful in supporting proposed interactions.|
|KEGG||Pathway mapping and visualisation is performed using the Kyoto Encyclopedia of Genes and Genomes (KEGG)|
|Protein Atlas||Additional experiments are required to confirm any hypotheses about phosphorylation events between specific kinase and substrate pairs. One way to do this is to use antibodies against the identified substrate or kinase....|
What do we do with your data?
Any data upladed by the user is kept confidential. We do not analyse, download or examine user data unless necessary for system maintenance or troubleshooting. We do not keep backups or archives and user data is automatically erased from our servers after 14 days unless a shorter retention period is specified upon search submission. Users are advised to download search results immediately after completing an analysis.
Do you have any questions? Would you like a new feature to be included into Phosphomatics? Let us know