Update: 2010 January 11

Welcome …

This is a free on-line resource developed by Kinexus Bioinformatics Corporation to foster the study of cell signalling systems to advance biomedical research in academia and industry. PhosphoNET presently holds data on more than 74,000 phosphorylation sites in over 12,400 human proteins that have been collected from the scientific literature and other reputable websites. Kinexus believes that the vast majority of mammalian proteins are phosphorylated. With the PhosphoNET Evolution module, this website also provides information about cognate proteins in up to 22 other species that may share these phospho-sites. PhosphoNET features direct links to several other useful websites, and will continue to expand to become a premier portal for phosphoproteomics information.

Role of Phosphorylation …

Protein phosphorylation is well recognized as the premier mode of post-translational regulation of proteins. Since the human genome encodes about 23,000 proteins, it is readily apparent from this SigNET Knowledgebase that more than half of the human proteins are confirmed to phosphorylated. Research at Kinexus is revealing that it is highly probable that the vast majority of proteins are in fact phosphorylatable, and there may be very few exceptions. Based on the number of tyrosine phosphorylated sites in PhosphoNET (i.e. >17,674) and the percentage of tyrosine phosphorylation sites relative to the total number of phospho-sites discovered in randomized studies (i.e. ~4%), we estimate that there are at least 450,000 human phospho-sites. The actual number is likely to be more than 500,000. Therefore, more than 84% of the true number of phospho-sites remain to be identified. Of the ~80,000 phospho-sites that have been demonstrated, functional information is available for only about 2%. Only about 0.85% of these phosphorylations have been correlated with an increase in enzymatic activity or a gain of function, whereas only 0.31% result in a decrease in enzymatic activity or a reduction of function. We believe that only a small percentage of the human phosphorylation sites directly regulate activities of proteins and control protein-protein interactions. It would appear that the major role of hyperphosphorylation of proteins is to facilitate their degradation by proteases. The challenge for the biomedical research community is to identify the most critical phosphorylation sites that regulate protein functions and serve as biomarkers of human disease. Kinexus is committed to the identification of these phospho-sites and the development of tools to permit their analysis in experimental model and clinical specimens. PhosphoNET is a free Internet resource that has been developed to facilitate this important endeavor.

Instructions …

PhosphoNET is designed to be fast and simple to navigate. You can search for target proteins if you know its Uniprot ID or its one of its common alias names. A list of possible options for proteins are generated by typing at least three letters of their name, and waiting for several seconds for a complete list to appear. Once a unique phosphoprotein webpage is created, you can click on the white buttons to the right of the phosphosite sequences to get more information that will appear in the white “Info Box” and the orange buttons to link to additional webpages. PhosphoNET Evolution is accessed by clicking on the orange buttons under the “Evol.” heading. Dark grey buttons are presently inactive. The optimum web browsers for using PhosphoNET are Internet Explorer and Firefox. There are some unresolved line alignment issues with Safari with PhosphoNET Evolution.

Coming Soon…

This website is a work in progress with limited financial assistance. At this juncture, PhosphoNET features two modules that lists basic information about human phospho-sites and their evolutionary conservation. Our goal is to consolidate this information and use it to predict additional human phosphorylation sites, their functionality and regulation. Later this year, we are aiming to launch a third module of PhosphoNET that predicts those protein kinases, SH2- and PTB-domain containing proteins that most like target these phosphosites. Quantitative information on several hundreds phosphorylation sites in hundreds of diverse cells and tissues is also available through our KiNET DataBank that is freely available. PhosphoNET is the first of several planned on-line knowledgebases that will become available from Kinexus Bioinformatics Corporation as part of our SigNET KnowledgeBank to accelerate signal transduction research. Additional knowledgebases for human protein kinases, phosphatases, adapter proteins, and stress proteins are also currently in development.

Advertising Opportunities …

To develop and sustain this free resource, we are seeking sponsorship from foundations and corporations. It is also possible for commercial vendors of signal transduction reagents and services to advertise their relevant products and services on this site. Interested parties should contact our Sales and Marketing Department at info@kinexus.ca or call toll free in North America 1-866-KINEXUS.

Some PhosphoNET Website Statistics …

• Total number of phosphosites: 74,473

• Percent serine phosphosites: 58.5%

• Percent of serine-proline phosphosites of total serine phosphosites: 26.8%

• Percent threonine phosphosites: 17.8%

• Percent of threonine-proline phosphosites of total threonine phosphosites: 27.9%

• Percent tyrosine phosphosites: 23.7%

•Total number of proteins represented: 12,400

• Average number phosphosites per protein: 6

• Median number phosphosites per protein: 2.0

• Number of phosphosites with some functional information: 1553

• Number of phosphosites that are activatory: 631

• Number of phosphosites that are inhibitory: 229

• Average Mr of phosphoproteins: 78,094 Da

• Median Mr of phosphoproteins: 56,956 Da

• Average number amino acids per protein: 698

• Median number amino acids per protein: 510