. Author manuscript; available in PMC: 2010 Apr 1.

Published in final edited form as: Pac Symp Biocomput. 2010:337–347. doi: 10.1142/9789814295291_0036

Table 3.

The observed rates of matches between amino acid substitutions and true and homology post-translational modification sites. Example: for N-linked glycosylation, out of 31 mutations that directly matched N-linked glycosylation sites, 4 were observed in the neutral set (Neutral) and 27 in the inherited disease set (Disease-I). The expected number of matches were 13.6 and 15.8, respectively. Blue color indicates lower-than-expected observed frequencies; red indicates higher-than-expected observed frequencies. P-values were calculated using the binomial distribution. The Bonferroni-corrected value of 5.6e-4 (n = 90) was used to assign statistical significance for each group.

Post-translational modification	Direct match; true sites						Direct and neighborhood match; homology sites
	Neutral		Disease-I		Disease-S		Neutral		Disease-I		Disease-S
	f_obs	P	f_obs	P	f_obs	P	f_obs	P	f_obs	P	f_obs	P

Phosphorylation	47/136		76/136		13/136		457/1218	2.0e-6	670/1218		91/1218	5.3e-5
N-linked glycosylation	3/28	2.2e-4	27/31	2.7e-5	0/31		70/306	8.3e-15	233/306	1.6e-19	3/306	1.8e-4
O-linked glycosylation	4/13		9/13		0/13		10/45		35/45	2.1e-4	0/45
Acetylation	1/8		7/8		0/8		12/91	2.4e-10	75/91	4.5e-10	4/91
Amidation	1/1		0/1		0/1		2/4		2/4		0/4

Hydroxylation	0/2		1/2		1/2		2/72	1.1e-15	68/72	6.6e-16	2/72
Proteolytic cleavage	7/29		22/29		0/29		36/120		84/120	1.9e-5	0/120
Methylation	0/4		4/4		0/4		6/20		12/20		2/20
Pyrrolidone carboxylic acid	1/1		0/1		0/1		2/2		0/2		0/2
Ubiquitination	0/0		0/0		0/0		2/24	1.7e-4	20/24		2/24

Carboxylation	0/29	4.8e-8	29/29	3.4e-9	0/29		1/63	6.3e-15	62/63	2.4e-17	0/63
SUMOylation	0/0		0/0		0/0		2/7		4/7		1/7
Palmitoylation	0/0		0/0		0/0		4/16		12/16		0/16
Sulfation	0/3		3/3		0/3		2/12		10/12		0/12
Myristoylation	0/1		1/1		0/1		1/3		2/3		0/3