Table 1.

Directional evolution of gene expression in pathways

Name	Statistic*	# Genes†	P‡	Annotation
A. Gene groups defined by coregulation in S. cerevisiae (14); 1.08 false-positive groups expected
Cluster_Histidine	−7	8	9.00E-05	Histidine biosynthesis
Node 73	71	349	0.001	Ribosome and translation
Cluster_NRG1	−7	12	0.002	Stress-induced transport
Cluster_Lysine	−5	8	0.006	Lysine biosynthesis
Node 45	−9	45	0.007	Respiration
B. Gene groups defined as the Biological Process categories from Gene Ontology; 0.53 false-positive groups expected
GO:0422540	79	269	1.0E-05	Ribosome biogenesis
GO:0016070	124	827	0.009	RNA metabolic process
GO:0006275	−8	56	0.01	Cellular 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.