About PhosphoNET ...
PhosphoNET is an open-access, online resource developed by Kinexus
Bioinformatics Corporation to foster the study of cell signalling systems
to advance biomedical research in academia and industry. PhosphoNET is the
worlds largest repository of known and predicted information on human
phosphorylation sites, their evolutionary conservation, the identities of
protein kinases that may target these sites and related phosphosites. PhosphoNET presently holds data on
over 950,000 known and putative phosphorylation sites (P-sites) in over 20,000
human proteins that have been collected from the scientific literature and other
reputable websites. Over 19%
of these phosphosites have been experimentally validated. The rest have been
predicted with a novel P-Site Predictor algorithm developed at Kinexus with
academic partners at the University of British Columbia and Simon Fraser
University.
With the PhosphoNET Evolution module, this website also provides information about cognate proteins in over 20 other species that may share these human phosphosites. This helps to define the most functionally important phosphosites as these are expected to be highly conserved in nature.
With the
Kinase Predictor module, listings are provided for the top 50 human protein
kinases that are likely to phosphorylate each of these phosphosites using
another proprietary kinase substrate prediction algorithm developed at Kinexus.
Our kinase substrate predictions are based on deduced consensus phosphorylation
site amino acid frequency scoring matrices that we have determined for each of
~500 different human protein kinases. The specificity matrices are generated
directly from the primary amino acid sequences of the catalytic domains of these
kinases, and when available, have proven to correlate strongly with substrate
prediction matrices based on alignment of known substrates of these kinases. The
higher the score, the better the prospect that a kinase will phosphorylate a
given site. Over 30 million kinase-substrate phosphosite pairs are quantified
in PhosphoNET. Kinexus Bioinformatics Corporation has the capability to test
most of these putative interactions in vitro for our clients.
With the Phosphosite Match module, we have identified those
phosphosites that show the greatest amino acid identity to a selected
target human phosphosite. This tool is useful to identify related
phosphosites that might be targeted the same protein kinases,
phosphatases and/or adapter proteins. This type of query might also
help identify potential off-targets for cross-reactive proteins that are
detected with phosphosite-specific antibodies that were generated to
recognize target phosphosites.
 
Role of Phosphorylation
Protein phosphorylation is well recognized as the premier
mode of post-translational regulation of proteins. The human genome encodes over
20,000 proteins, and more than two thirds of these proteins have already been
shown to be subject to phosphorylation. Research at Kinexus has revealed the
vast majority of proteins are in fact phosphorylatable, and there may be very
few exceptions. Based on the number of experimentally confirmed tyrosine
phosphorylated sites in PhosphoNET (i.e. >36,000) and the percentage of tyrosine
phosphorylation sites relative to the total number of phosphosites discovered
in randomized studies (i.e. ~4%), we originally estimated that there are at
least 500,000 human phosphosites. With our proprietary P-site Predictor
algorithm, we have been able to identify over 800,000 new putative human phosphosites.
Of the ~180,500 phosphosites that have been demonstrated,
functional information is available for only about 1%. Only about 0.85% of these
phosphorylations have been correlated with an increase in enzymatic activity or
a gain of function, whereas only 0.3% 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 actually 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 important phosphosites 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 protein
if you know its UniProt ID, International Protein ID, or one of its common alias
names. You can also search PhosphoNET with the complete 15 amino acid sequence
(in single letter code) surrounding a phosphosite (the phosphorylated amino
acid should be defined in the 8th position). A list of possible options for
proteins are generated by typing at least three letters of their name or
identification number, and waiting for a few seconds for a complete list to
appear. Once a unique phosphoprotein webpage is created, you can hover your
cursor over the coloured buttons to the right of the phosphosite sequences to
get more information that will appear next to the button. If the button is
clicked, this information will appear in the white Info Box. Clicking on the
orange buttons activates links to additional webpages. PhosphoNET Evolution,
PhosphoNET Kinase Predictor, and PhosphoNET Phosphosite Match are accessed by clicking on the orange buttons under
the Evol., Kinase Pred., and "P-Site Match" headings, respectively. Dark grey buttons are
presently inactive. The optimum web browsers for using PhosphoNET are Internet
Explorer, Firefox and Safari.
Funding and Advertising Opportunities
To develop and sustain this free resource, we are seeking sponsorship from foundations and corporations. We gratefully acknowledge financial grant support for PhosphoNET from the National Research Council of Canada Industrial Assistance Program and the Natural Sciences and Engineering Research Council of Canada.
It is 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: 966,817
Total number of experimentally-confirmed phosphosites: 177,424
Percent
serine phosphosites: 56.0%
Percent
threonine phosphosites: 23.5%
Percent
tyrosine phosphosites: 20.4%
Total
number of proteins represented: 22,698
Average
number phosphosites per protein: 42.6
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: 61,520 Da
Median Mr
of phosphoproteins: 46,000 Da
Average
number amino acids per phosphoprotein: 552
Median
number amino acids per phosphoprotein: 410
Copyright © 2019 Kinexus Bioinformatics Corporation