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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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Propagated PTMs. Users can choose to display the propagated PTMs by clicking in the checkbox in the display menu (A). Here, we show the protein Sox2 in Pan troglodytes (A) which had no PTMs experimentally validated while several are predicted from orthologs, mainly acetylations from the mouse copy of the protein (B) and phosphorylations from human (C). Those PTMs were also propagated between mouse and human (not displayed in the figure).
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Figure 2: Propagated PTMs. Users can choose to display the propagated PTMs by clicking in the checkbox in the display menu (A). Here, we show the protein Sox2 in Pan troglodytes (A) which had no PTMs experimentally validated while several are predicted from orthologs, mainly acetylations from the mouse copy of the protein (B) and phosphorylations from human (C). Those PTMs were also propagated between mouse and human (not displayed in the figure).

Mentions: Thus, although propagated PTMs should be taken with much caution and used only for exploratory analyses, they exhibit a reasonable overlap with known PTMs as a good indicator for their reliability. By this simple exercise we obtained 1 347 165 sites with a modification signal propagated from verified PTMs allowing us to produce post-translational information for species that otherwise count with almost none experimental data (Figure 2).


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)

Propagated PTMs. Users can choose to display the propagated PTMs by clicking in the checkbox in the display menu (A). Here, we show the protein Sox2 in Pan troglodytes (A) which had no PTMs experimentally validated while several are predicted from orthologs, mainly acetylations from the mouse copy of the protein (B) and phosphorylations from human (C). Those PTMs were also propagated between mouse and human (not displayed in the figure).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: Propagated PTMs. Users can choose to display the propagated PTMs by clicking in the checkbox in the display menu (A). Here, we show the protein Sox2 in Pan troglodytes (A) which had no PTMs experimentally validated while several are predicted from orthologs, mainly acetylations from the mouse copy of the protein (B) and phosphorylations from human (C). Those PTMs were also propagated between mouse and human (not displayed in the figure).
Mentions: Thus, although propagated PTMs should be taken with much caution and used only for exploratory analyses, they exhibit a reasonable overlap with known PTMs as a good indicator for their reliability. By this simple exercise we obtained 1 347 165 sites with a modification signal propagated from verified PTMs allowing us to produce post-translational information for species that otherwise count with almost none experimental data (Figure 2).

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