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Using this classification, 63% of the sites in our phosphoproteome were accurately localized (class I, Figure S1D) (median localization probability for all sites was 0.96).
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Phosphorylation sites with a localization probability of ≥0.75 were considered to be localized.
We first theoretically prove that the proposed scheme can improve the localization probability and accuracy.
Finally, extensive experimental results demonstrate that our method outperforms the fixed anchor-based methods by 20%45%% in terms of localization accuracy and 20%50%% in terms of localization probability.
False discovery rate (FDR) was adjusted to <1% and the site localization probability was set as >0.75.
Our algorithm achieves very high localization probability when compared with existing cluster formation algorithms, at no additional cost.
Phosphorylation sites with localization probability <0.25 were discarded.
For class II sites, localization probability was between 0.75 and 0.25.
The reported foci were treated as localization probability distributions centered at the given Y and Z peak coordinates [36].
Phosphorylation sites with a localization probability <0.25 were discarded.
All confirmed sites of phosphorylation contained a localization probability >75% and were reviewed manually.
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