Table 1.
Tests for Directional Regulatory Change between Saccharomyces cerevisiae and S. paradoxus Expression in Coregulated Gene Groups.
| Namea | Number of Genes | ΣRSc/Sp;totalb | P Totalc | P cisd | P transe | Annotation |
|---|---|---|---|---|---|---|
| Cluster_adata-CalciumSpecific* | 47 | −25.8 | <0.0002 | 0.0056 | 0.001 | Membrane proteins |
| Node 7 | 183 | 85.8 | <0.0002 | 0.0506 | <0.0002 | Heat-shock proteins, stress |
| Cluster_PUF3 | 193 | −46.3 | <0.0002 | 0.2372 | <0.0002 | Mitochondrion |
| Node 73 | 392 | −140.1 | <0.0002 | 0.4644 | <0.0002 | Ribosome, translation |
| Cluster_ManualHAP1targets | 36 | −28.2 | <0.0002 | 0.5044 | <0.0002 | Respiration |
| Cluster_HAP5 | 24 | −12.6 | 0.0072 | 0.0114 | 0.108 | Respiration |
| Cluster_Vacuole | 56 | 17.1 | 0.0114 | 0.019 | 0.0434 | Vacuole |
| Cluster_PHD1 | 27 | −12.2 | 0.0114 | 0.0618 | 0.0232 | Stress, signaling |
| Cluster_SWI4 | 48 | −16.1 | 0.0136 | 0.071 | 0.0252 | Cell cycle |
| Node 6 | 10 | 7.0 | 0.0178 | 0.1296 | 0.003 | Protein modification and breakdown |
| Cluster_ARG80 | 18 | −9.1 | 0.0204 | 0.1622 | 0.01 | Amino acid biosynthesis |
a Gene groups defined by Gasch et al. (2004). Results from analysis of the membrane protein regulon are denoted with an asterisk.
b Sum, across genes in the indicated regulon, of the log2 ratio of expression in S. cerevisiae to expression in S. paradoxus, when each species was grown in independent culture (RSc/Sp;total).
c Significance of a two-sided resampling test relative to the genomic null for an extreme value of the sum, across genes in the indicated regulon, of the log2 ratio of expression in S. cerevisiae to expression in S. paradoxus, when each species was grown in independent culture (RSc/Sp;total). Shown are all groups meeting a significance level where 2.1 groups would be expected under the null.
d Significance of a one-sided resampling test relative to the genomic null for an extreme value of the sum, across genes in the indicated regulon, of the log2 ratio of the expression of the S. cerevisiae allele to that of the S. paradoxus allele in an interspecific hybrid.
e Significance of a one-sided resampling test relative to the genomic null for an extreme value of the sum, across genes in the indicated regulon, of the log2 ratio of the effects of trans-acting regulatory variation between S. cerevisiae and S. paradoxus, where the latter is derived from expression measurements of the interspecific hybrid and of parent strains grown independently (Tirosh et al. 2009).