Table 1 Non-random distribution of stress-related genes in budding yeast
From: Non-random clustering of stress-related genes during evolution of the S. cerevisiae genome
Dataset | Number of genes in dataset | Number of genes in dataset within 1 kb ORC binding site(% genes in dataset) | Number of genes in starvation-induced clusters (% genes in dataset) | Number of genes in starvation-repressed clusters (% genes in dataset) | Number of potentially silenced genes (% genes in dataset) |
|---|---|---|---|---|---|
all genes | 7104 | 1164 (16.4%) | Â | Â | Â |
orc2-1 -induced genes | 524 | 151 (28.8%) (+) | 205 (38.9%) (+) | 43 (8.0%) (-) | Â |
potentially silenced genes | 2111 | 431 (20.4%) (+) | 644 (30.5%) (+) | 238 (11.3%) (-) | 2111 (100%) |
Starvation and other stress-related genes | |||||
starvation-induced genes | 2213 | 443 (20.0%) (+) | 1073 (48.5%) (+) | 137 (6.2%) (-) | 1086 (51.4%) (+) |
starvation-induced clusters | 1404 | 323 (23.1%) (+) | 1404 (100%) | 32 (2.3%) (-) | 644 (45.9%) (+) |
starvation-repressed genes | 2020 | 224 (12.1%) (-) | 105 (5.2%) (-) | 1091 (54.0%) (+) | 296 (19.6%) (-) |
starvation-repressed clusters | 1416 | 185 (13.0%) (-) | 32 (2.3%) (-) | 1416 (100%) | 238 (16.8%) (-) |
starvation-induced genes†| 2042 | 400 (20%) (+) | 676 (33.1%) (+) | 148 (7.2%) (-) | 999 (49.0%) (+) |
MMS)-induced genes | 452 | 93 (20.6%) (+) | 181 (40.0%) (+) | 55 (12.2%) (-) | 210 (46.4%) (+) |
MMS)-repressed genes | 217 | 33 (15.2%*) (-) | 20 (9.2%) (-) | 87 (40.1%) (+) | 26 (12.0%) (-) |
HU-induced genes | 116 | 24 (20.5%*) (+) | 41 (35.3%) (+) | 14 (12.1%) (-) | 62 (53.4%) (+) |
HU-repressed genes | 71 | 7 (9.8) (-) | 14 (19.7%*) (-) | 29 (40.8%) (+) | 21 (29.6%*) (-) |
H 2 0 2 -induced genes | 1379 | 255 (18.5%*) (+) | 434 (31.5%) (+) | 167 (12.1%) (-) | 598 (43.4%) (+) |
H 2 0 2 -repressed genes | 1536 | 235 (15.3%) (-) | 224 (14.6%) (-) | 457 (29.8%) (+) | 479 (31.1%*) (+) |
ESR-induced genes | 282 | 63 (22.3%) (+) | 123 (43.6%) (+) | 14 (5.0%) (-) | 153 (54.2%) (+) |
ESR-repressed genes | 585 | 75 (12.8%) (-) | 14 (2.4%) (-) | 322 (55%) (+) | 32 (5.5%) (-) |
Essential growth genes and genes required for stress resistance in cycling cells | |||||
Genes essential for growth | 1106 | 130 (11.8%) (-) | 106 (9.6%) (-) | 355 (32.1%) (+) | 161 (14.6%) (-) |
MMS-resistance | 103 | 11 (10.7%) (-) | 6 (5.8%) (-) | 20 (19.4%*) (-) | n.d. |
Camptothecin resistance | 83 | 8 (9.6%) (-) | 7 (8.4%) (-) | 14 (16.9%*) (-) | n.d. |
HU-resistance | 136 | 13 (9.6%) (-) | 9 (6.6%) (-) | 28 (20.6%*) (+) | n.d. |
H 2 0 2 -resistance | 123 | 15 (12.2%) (-) | 13 (10.6%) (-) | 24 (19.5%*) (-) | n.d. |
Oxidative stress resistance | 685 | 87 (12.8%) (-) | 95 (13.9%) (-) | 158 (23.0%*) (+) | n.d. |
UV-resistance | 307 | 34 (11.1%) (-) | 30 (9.8%) (-) | 56 (18.2%) (-) | n.d. |
All stress-resistance | 974 | 115 (11.8%) (-) | 129 (13.2%) (-) | 208 (21.3%*) (+) | 251 (25.8%) (-) |
Slowly and rapidly evolving paralogues | |||||
slowly evolving paralogues | 115 | 15 (13.0%) (-) | 22 (19.1%*) (-) | 34 (29.6%*) (+) | 19 (16.5%) (-) |
rapidly evolving paralogues | 115 | 26 (22.6%) (+) | 30 (26.0%*) (+) | 16 (13.9%) (-) | 57 (49.6%) (+) |