Table 1.

Directional evolution of gene expression in pathways

NameStatistic*# GenesPAnnotation
A. Gene groups defined by coregulation in S. cerevisiae (14); 1.08 false-positive groups expected
 Cluster_Histidine−789.00E-05Histidine biosynthesis
 Node 73713490.001Ribosome and translation
 Cluster_NRG1−7120.002Stress-induced transport
 Cluster_Lysine−580.006Lysine biosynthesis
 Node 45−9450.007Respiration
B. Gene groups defined as the Biological Process categories from Gene Ontology; 0.53 false-positive groups expected
 GO:0422540792691.0E-05Ribosome biogenesis
 GO:00160701248270.009RNA metabolic process
 GO:0006275−8560.01Cellular aromatic compound metabolic process
  • Listed are the top-scoring gene groups with sign imbalance in cis-regulatory variation. Results for all groups are given in Table S8.

  • *Directional differential expression statistic measuring the imbalance in the signs of cis-regulatory variants within gene groups, defined as the sum of the directional scores of the group members (1 for a gene significantly up-regulated in S. bayanus for both biological replicates, −1 for a gene significantly up-regulated in S. cerevisiae, and 0 otherwise).

  • Total number of genes in each group for which a directional score was available.

  • Resampling-based P value assessing the significance of directional cis-regulatory expression variation in each group.