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Search for a specific protein in the Platelet Interactome


(Example: vasp)

 

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Get detailed protein information focusing on various characteristics and extract interaction networks

 

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About

Tutorial

  1. Where do I begin?
  2. Where does the data come from?
  3. Description of the proteins
  4. Phosphorylation and kinase information
  5. How to optimally use advanced search options?
  6. How to extract subnetworks for proteins of interest and download files to visualize in Cytoscape?
  7. Images not printing when trying to print. What do I do?
  8. Still having questions! What do I do?

4a. Phosphorylation information


The information about the protein's phosphorylation state appears when the target protein is submitted in the search bar. The icon ST stands for "serine/threonine" and the icon Y stands for "tyrosine" residue phosphorylation.

To distinguish between platelet phosphorylations (detected in platelets) and human phosphorylation sites (detected in any human cell), the user should pay attention to the color of the S, T and Y icons.

  • Platelet phosphorylation sites, in dark blue or red, are extracted from a platelet mass spectrometry phosphoproteome study by Zahedi et al1, therefore they are platelet-specific (the protein is found phosphorylated in platelets).
  • Human phosphorylation sites, in light blue or red, are listed in HPRD and PhosphoSite for each protein. They are highly relevant, because of the manual curation of phosphorylation information, but it should be kept in mind that these phosphorylations are found in various cell types and may not be platelet-specific.


    • 4b. Kinase information


    Kinase-substrate information was extracted from HPRD and PhosphoSite and is depicted with a red arrow. This data is available only for the human phosphorylation sites. For some of the platelet phosphorylation sites, there is a kinase prediction displayed on the description page (Question 3) of the protein, which was calculated using bioinformatical approaches (NetworKIN algorithm)2. Kinase predictions are depicted with a blue arrow.

    1 Zahedi, R.P. et al. Phosphoproteome of resting human platelets. J Proteome Res 7, 526--534 (2008).
    2 Miller, M.L. et al. Linear motif atlas for phosphorylation-dependent signaling. Sci Signal 1, ra2 (2008).



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