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
(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

*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.

Harrison and Gerstein Genome Biology 2003 4:R40   doi:10.1186/gb-2003-4-6-r40