Table 3.

Odds ratio of optimal codon usage between exposed-aggregation-prone and exposed-non-aggregation-prone sites, between buried-aggregation-prone and buried-non-aggregation-prone sites, between exposed-aggregation-prone and buried-non-aggregation-prone sites, and between buried-aggregation-prone and exposed-non-aggregation-prone sites for each amino acid

	E. coli				S. cerevisiae				D. melanogaster				M. musculus
AA	EA-EN	BA-BN	EA-BN	BA-EN	EA-EN	BA-BN	EA-BN	BA-EN	EA-EN	BA-BN	EA-BN	BA-EN	EA-EN	BA-BN	EA-BN	BA-EN
Ala	1.02	1.05	1.07	0.93	0.70	0.92	0.57(**)	0.99	1.45(*)	1.08	1.25	1.22	–	–	–	–
Arg	1.02	1.04	1.06	1.01	1.57	1.13	1.56	0.90	1.31	0.93	1.28	1.22	1.33(*)	1.16	1.26	1.44*
Asn	1.27*(*)	1.02	0.94	1.46***	0.88	1.12	0.94	1.16	1.17	1.63*(*)	1.28	1.57*(*)	1.14	1.12	0.88	1.41***
Asp	1.15	1.18	1.05	1.22(*)	1.03	0.84	1.10	0.78	1.65***	1.64*(*)	1.87***	1.50*(*)	1.11	1.23	1.08	1.30*(*)
Cys	0.78	1.03	1.13	0.83	1.60	0.76	0.29(*)	0.84	0.54	1.03	1.04	0.82	–	–	–	–
Gln	1.02	0.89	0.84	1.13	1.08	1.14	1.31	1.42	0.75	0.94	0.84	0.91	1.04	1.27	0.98	1.42*(*)
Glu	0.96	1.00	0.90	1.07	1.01	1.35	1.15	1.26	0.91	0.82	0.97	0.91	0.89	1.05	0.83	1.05
Gly	1.24(*)	1.31**(*)	1.19	1.37***	0.94	0.94	0.70(*)	1.32(*)	0.92	1.11	0.97	1.10	1.11	1.25**(*)	1.08	1.23**(*)
His	1.33(*)	1.50**(*)	1.25	1.33(*)	1.59	0.99	1.72	1.05	0.93	1.63(*)	1.91(*)	1.10	1.30(*)	1.15	1.17	1.26
Ile	1.36(*)	1.09	1.36(**)	1.10	0.94	0.68*(*)	1.23	1.00	1.27	0.93	1.02	1.06	1.07	1.15*	1.05	1.24*(*)
Leu	0.91	0.81***	0.82(*)	0.96	0.84	1.03	0.86	1.18	0.87	1.07	0.82	1.14	0.76*(*)	0.87**	0.82(*)	0.86*(*)
Lys	–	–	–	–	0.73	0.83	0.63(*)	0.90	0.73(*)	0.47(*)	0.87	0.72	1.08	1.36(*)	1.08	1.42*(*)
Phe	0.94	1.03	1.02	1.03	1.03	1.10	0.78	1.15	0.71	1.02	0.68	0.82	0.85	1.19**	1.03	1.18
Pro	1.58	0.69	1.59	0.83	2.35	0.18	2.74	0.19	2.88	0.17	5.08	0.21	0.56	0.51	0.63	0.44
Ser	1.18	1.19(*)	0.88	1.70***	0.96	1.53*(*)	0.98	1.58**(*)	1.10	0.74(*)	0.87	1.01	1.09	1.24*(*)	0.90	1.40***
Thr	1.28*(*)	1.23**	1.07	1.55***	0.91	0.93	0.82	1.06	1.09	1.36*(*)	1.09	1.40*(*)	1.31**(*)	1.20*(*)	1.12	1.37***
Tyr	1.25	1.27**	1.30(*)	1.06	0.79	1.04	1.13	1.01	1.18	1.30	1.12	1.26	–	–	–	–
Val	0.94	0.86**	0.94	0.75***	1.27	1.27(*)	1.24	1.53*(*)	1.01	1.07	0.77	1.21	1.05	0.96	0.91	1.03
Overall	1.13***	1.03	1.02	1.13***	0.95	1.03	0.93	1.15**(*)	1.06	1.08*(*)	1.06	1.15***	1.08*(*)	1.08***	1.00	1.19***

Note. —AA: amino acid; EA: exposed and aggregation-prone sites; BN: buried and non-aggregation-prone sites; BA: buried and aggregation-prone sites; EN: exposed and non-aggregation-prone sites; -: no optimal codon. Significance levels:

^***P < 0.001;

^**P < 0.01;

^*P < 0.05.

Significance levels in parentheses disappear after correction for multiple testing.