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Table 2 Abundance of biased regions that have biases at the same level as the Q and N biases in the four budding-yeast prions

From: A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes

(a) Biases in terms of total number of regions*
Rank Budding yeast Fission yeast Fruit fly Nematode Arabidopsis Human
1 S 108 [1] S 74 Q 725 (20.7) P 494 P 345 P 549
2 Q 104 [8] (17.8) P 40 G 400 G 448 E 292 E 322
3 N 73 [1] (12.5) E 37 P 359 E 286 G 242 C 302
4 E 68 [18] T 32 S 327 Q 270 (8.9) Q 153 (6.0) G 294
5 T 58 Q 17 (5.6) A 264 C 220 C 150 S 233
6 P 37 [1] G 17 H 231 T 199 S 134 K 188
7 D 35 K 16 E 212 K 184 D 90 Q 176 (5.9)
8 K 24 [9] A 15 T 188 S 146 K 86 A 136
9 G 20 C 13 K 170 R 132 R 81 R 83
10 A 19 [1] R 11 N 144 (4.1) A 102 L 56 H 80
11 H 8 V 6 C 144 D 55 A 56 T 59
12 C 8 H 6 R 118 H 46 H 47 D 49
13 R 6 M 5 D 74 N 40 (1.3) Y 28 L 31
14 M 5 N 4 (1.3) L 47 F 17 N 28 (1.1) M 23
15 L 5 F 4 Y 28 Y 16 T 17 F 21
16 V 3 L 3 M 24 M 15 M 11 V 18
17 Y 2 D 2 V 22 L 11 V 8 N 15 (0.6)
18 F 2 Y 1 F 8 V 6 W 5 Y 13
19 W 0 W 0 W 5 I 5 F 3 W 11
20 I 0 I 0 I 5 W 1 I 1 I 10
  Total 585 Total 303 Total 3,495 Total 2,693 Total 1,833 Total 2,613
(b) Biases in terms of total number of residues
Rank Budding yeast Fission yeast Fruit fly Nematode Arabidopsis Human
1 S 10,630 S 9,035 Q 39,186 (16.3) P 31,917 E 23,229 P 44,427
2 T 5,900 T 5,805 S 31,936 E 31,216 P 21,124 E 27,352
3 E 4,704 P 2,887 P 29,345 G 28,192 G 13,462 S 26,363
4 Q 3,924 (10.4) E 2,657 G 24,320 Q 18,126 (8.9) S 10,313 G 22,131
5 N 3,745 (10.0) A 1,854 E 23,384 T 15,994 L 9,459 C 16,681
6 P 2,049 G 1,669 A 14,730 S 15,262 C 6,852 K 15,459
7 K 1,910 C 1,185 K 14,448 C 15,224 Q 6,835 (6.0) Q 12,156 (5.9)
8 D 1,292 Q 1,107 (3.6) T 12,560 K 14,518 K 6,122 A 9,587
9 G 961 L 1,087 C 10,067 A 9,124 R 4,061 T 5,667
10 A 916 V 851 L 9,331 R 7,501 A 3,244 L 5,646
11 L 554 K 680 R 6,847 D 6,950 D 3,176 R 5,165
12 C 256 N 486 (1.6) H 6,302 N 2,606 (1.3) Y 2,315 H 3,189
13 R 204 R 425 D 5,695 H 2,361 N 1,259 (1.1) V 2,964
14 H 195 F 257 N 5,690 (2.4) L 1,352 H 1,044 D 2,085
15 M 163 H 238 V 2,651 F 827 T 697 N 1,714 (0.8)
16 F 94 M 217 Y 1,179 M 746 V 549 F 1,433
17 V 90 D 127 M 915 Y 692 M 287 M 1,081
18 Y 33 Y 60 I 798 V 608 F 221 I 924
19 W 0 I 0 F 667 I 404 W 162 Y 617
20 I 0 W 0 W 147 W 42 I 16 W 541
  Total 37,620 Total 30,627 Total 240,198 Total 203,662 Total 114,427 Total 205,182
(c) Ratios of numbers for Q-rich and N-rich biased regions compared to the ratios of their overall abundances as residues§
  Budding yeast Fission yeast Fruit fly Nematode Arabidopsis Human
RQ/N (total residues) 1.05   2.28   6.89   6.96   5.43   7.09  
RQ/N (total regions) 1.42   4.25   5.03   6.75   5.46   11.73  
Q/N (composition) (0.039/0.061) = 0.64   (0.038/0. 052) = 0.73   (0.052/0 .047) = 1.12   (0.041/ 0.049 = 0.83   (0.035/ 0.044 = 0.79   (0.047/ 0.037 = 1.28  
  1. *The total numbers of regions that have a compositional biased LPS with Pbias < 1 × 10-13. The number of LPSs for a particular compositional bias in the budding yeast proteome that overlap a region assigned as coiled coil by the MULTICOIL program [22]. The total numbers of bias residues (for example, total number of serines for a serine bias) for all of the regions tallied for part (a) of the table. § RQ/N is the ratio of the number of Q-rich regions to N-rich regions as listed in parts (a) and (b) of the table. The overall abundance of the residues is simply the fraction of the total proteome that is either Q or N.