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Table 4 Manually verified relationships in the validation and test set with ensemble prediction standard deviation less than interaction-wise threshold and predicted confidence greater than interaction-wise threshold, taking the precision to 100.0

From: Large-scale protein-protein post-translational modification extraction with distant supervision and confidence calibrated BioBERT

PubMed Phrases describing relationships in the abstract Label Prediction
Validation
12150926 mTOR (P42345)-catalyzed phosphorylation of 4EBP1 (Q13541) in vitro phosphorylation phosphorylation
15733869 SGK (O00141) physically associates with CREB (P16220) and SGK (O00141) phosphorylates it on serine 133 phosphorylation phosphorylation
15557335 Src (P12931) phosphorylated Alix (Q8WUM4) at a C-terminal phosphorylation phosphorylation
15527798 Phosphorylation of MDM2 (Q00987) by the protein kinase AKT (P31749) phosphorylation phosphorylation
10864201 Radiation-induced phosphorylation of p53 (P04637) protein at serine 15, largely mediated by ATM (Q13315) kinase Phosphorylation phosphorylation
24548923 Akt (P31749)-mediated phosphorylation of Carma1 (Q9BXL7) phosphorylation phosphorylation
19407811 BubR1 (O60566) forms a complex with PCAF (Q92831) and is acetylated at lysine 250 acetylation acetylation
Test
21920476 coilin (P38432) is phosphorylated in Ser184 by both VRK1 (Q99986) phosphorylation phosphorylation
19424295 Previous studies of cofilin (P23528) have shown that it is phosphorylated primarily by the LIM domain kinases Limk1 (P53667) phosphorylation phosphorylation
22726438 FGFR2 (P21802) phosphorylates tyrosine residues on Grb2 (P62993) phosphorylation phosphorylation
11154276 Akt (P31749) decreased ASK1 (Q99683) kinase activity stimulated by both oxidative stress and overexpression in 293 cells by phosphorylating a consensus Akt (P31749) site at serine 83 of ASK1 (Q99683) phosphorylation phosphorylation
25605758 Phosphorylation of Rab5b (P61020) by LRRK2 (Q5S007) also exhibited phosphorylation phosphorylation
20856200 Binding of AKT (P31749) (tail region) to Vim (P08670) (head region) results in Vim (P08670) Ser39 phosphorylation phosphorylation phosphorylation
21986944 MAK (P20794) associates with CDH1 (P12830) (FZR1 (Q9UM11), fizzy/cell division cycle 20 related 1) and phosphorylates CDH1 (P12830) Negative phosphorylation
15862297 HDM2 (Q00987) phosphorylation by Chk2 (O96017) doubles in the presence of p53 (P04637) Negative phosphorylation
21887822 Hsp70 (P34932) is phosphorylated by Plk1 (P53350) Negative phosphorylation
  1. The bold highlights where the mentions of participating proteins
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BMC Bioinformatics

ISSN: 1471-2105

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