  The likelihood of O-GlcNAc glycosylation in human proteins is predicted using
the ridge regression estimated linear probability model (LPM). To achieve this,
sequences from three similar post-translational modifications (PTMs) of
proteins occurring at, or very near, the S or T site are analyzed:
N-glycosylation, O-mucin type (O-GalNAc) glycosylation, and phosphorylation.
Results found include: 1) The consensus composite sequon for O-glycosylation
does NOT have W on either side of the glycosylation site. 2) The same holds for
the consensus sequon for phosphorylation. 3) For LPM estimation, N-glycosylated
sequences are found to be good approximations to non-O-glycosylatable
sequences. 4) The selective positioning of an amino acid along the sequence,
differentiates the PTMs of proteins. 5) Some N-glycosylated sequences are also
phosphorylated at the S or T site. 6) ASA values for N-glycosylated sequences
are stochastically larger than those for O-GlcNAc glycosylated sequences. 7)
Structural attributes (beta turn II, II', helix, beta bridges, beta hairpin,
and the phi angle) are significant LPM predictors of O-GlcNAc glycosylation.
The LPM with sequence and structural data as explanatory variables yields a
Kolmogorov-Smirnov (KS) statistic value of 99%. 8) With only sequence data, the
KS statistic erodes to 80%, underscoring the germaneness of structural
information, which is sparse on O-glycosylated sequences. With 50% as the
cutoff probability for predicting O-GlcNAc glycosylation, this LPM mispredicts
21% of out-of-sample O-GlcNAc glycosylated sequences as not being glycosylated.
The 95% confidence interval around this mispredictions rate is 16% to 26%
