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PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.

Minguez P, Letunic I, Parca L, Garcia-Alonso L, Dopazo J, Huerta-Cepas J, Bork P - Nucleic Acids Res. (2014)

Bottom Line: These two processes are interdependent and together are responsible for the function of the protein in a particular cell state.Several databases focus on the prediction and compilation of protein-protein interactions (PPIs) and no less on the collection and analysis of protein post-translational modifications (PTMs), however, there are no resources that concentrate on describing the regulatory role of PTMs in PPIs.In total, we report 8 million associations of PTMs regulating single proteins and over 9.4 million interplays tuning PPIs.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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Visualization of functional associations between PTMs in interacting proteins. Users can explore the regulation of the interactions where their favorite protein is involved (A). We implemented a network viewer where all its interactions are displayed (B). Every partner in the network opens the ‘PPI view’, a framework to explore the functional associations found between PTMs from both proteins (C).
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Figure 4: Visualization of functional associations between PTMs in interacting proteins. Users can explore the regulation of the interactions where their favorite protein is involved (A). We implemented a network viewer where all its interactions are displayed (B). Every partner in the network opens the ‘PPI view’, a framework to explore the functional associations found between PTMs from both proteins (C).

Mentions: As the main novelty in visualization we have implemented a flash-based network view integrated into our interactive graphic interface where users can explore the network neighborhood centered on their favorite protein and jump to the ‘PPI view’ (Figure 4). There, the two proteins are shown facing each other and every pair of known or predicted associated PTMs may be further analyzed clicking on the channels pop-ups where extra information about every source of evidence is displayed.


PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.

Minguez P, Letunic I, Parca L, Garcia-Alonso L, Dopazo J, Huerta-Cepas J, Bork P - Nucleic Acids Res. (2014)

Visualization of functional associations between PTMs in interacting proteins. Users can explore the regulation of the interactions where their favorite protein is involved (A). We implemented a network viewer where all its interactions are displayed (B). Every partner in the network opens the ‘PPI view’, a framework to explore the functional associations found between PTMs from both proteins (C).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383916&req=5

Figure 4: Visualization of functional associations between PTMs in interacting proteins. Users can explore the regulation of the interactions where their favorite protein is involved (A). We implemented a network viewer where all its interactions are displayed (B). Every partner in the network opens the ‘PPI view’, a framework to explore the functional associations found between PTMs from both proteins (C).
Mentions: As the main novelty in visualization we have implemented a flash-based network view integrated into our interactive graphic interface where users can explore the network neighborhood centered on their favorite protein and jump to the ‘PPI view’ (Figure 4). There, the two proteins are shown facing each other and every pair of known or predicted associated PTMs may be further analyzed clicking on the channels pop-ups where extra information about every source of evidence is displayed.

Bottom Line: These two processes are interdependent and together are responsible for the function of the protein in a particular cell state.Several databases focus on the prediction and compilation of protein-protein interactions (PPIs) and no less on the collection and analysis of protein post-translational modifications (PTMs), however, there are no resources that concentrate on describing the regulatory role of PTMs in PPIs.In total, we report 8 million associations of PTMs regulating single proteins and over 9.4 million interplays tuning PPIs.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.

Show MeSH