PlateletWeb is a comprehensive systems biology tool, which allows a thorough analysis of HUMAN platelet and non-platelet proteins, their interactions, phosphorylation state and physical characteristics. The database contains validated experimental data on the platelet proteome and phosphoproteome, along with literature-derived information from HPRD (Human Protein Database Version 9.0) and PhosphoSite. It is the first database of its kind, which gives the opportunity for extracting interactive subnetworks of proteins on a platelet and non-platelet level. The user can choose between regular search of a specific protein of interest OR advanced search providing detailed information.
Search
In the search field on the left side of the window, just type in the name of the protein you are interested in and click on the "SUBMIT" button in order to get the protein related information. A list of suggestions appears as a drop-down menu to help the user find the right entry.
This retrieves the list of proteins matching your search term. In our example, our search term is "VASP" and so we got the proteins matching VASP as output.
The output, apart from listing the similar proteins, also provides information about the platelet and non-platelet interactions of each protein. Additionally, it supplies the level of protein detection (Proteome Level, Transcriptome Level (SAGE) or Both). It is also possible to click on the protein link in order to view additional information about the protein. Human phosphorylation sites and platelet phosphorylation sites are depicted using the symbols S, T and Y (for further details, see legend).
Click on "platelet interacting proteins" to view the list of platelet interactions (In the picture, a subset of the proteins are shown).
Alternatively, you can also click on "Total interacting proteins" for the complete list of interactions with this protein.
It is also possible to sort the list by clicking on the title of each column, thereby ordering proteins by their level of detection, phosphorylation state or alphabetically according to the gene symbol.
To view in picture format:
On the top of the interactions page, you will find a link which leads to the graphical representation of all retrieved interactions with
the searched protein.
What Next:
Using these links, you can either view and save the image in the pdf (Adobe Reader) format or alternatively download the information to view in Cytoscape.
The information on "How to view the downloaded files in Cytoscape" can be found in Question 6 of this tutorial.
Finally,
By providing the name of the protein, one can easily navigate through all its interactions, get the complete description, view and/or download the network graph associated with it. Apart from this, there is always the possibility of searching for proteins with their physical characteristics (using advanced search), download the subnetwork for a specific set of proteins (Cytoscape Download), and retrieve the complete information about their phosphorylation state, and if the proteins are kinases, their phosphorylation targets (for further details, see Question 3 of this tutorial).
