Table 2 . The correlation between gene expression and pleiotropy in Saccharomyces cerevisiae.

Data set	rSpearman	P	rPearson	P	ngenes	ntraits
Dudley et al. (2005)	0.059	0.116	0.071	0.119	698	21
Ohya et al. (2005)	0.077	0.0004	0.087	0.0002	1792	254
CYGD: phenotypic	−0.017	0.52	0.0095	0.56	1381	142
CYGD: functional	0.046	0.0006	0.027	0.104	5192	456
GO: biological processes	0.059	<0.0001	0.034	0.030	5160	2294
GO: molecular functions	0.064	<0.0001	0.033	0.037	5160	1747
GO: cellular components	0.193	<0.0001	0.173	<0.0001	5160	649
GO: all categories	0.127	<0.0001	0.106	<0.0001	5160	4690

Estimates of gene pleiotropy are obtained from different sources (leftmost column). Dudley et al. (2005) report significant growth defects for 774 nonessential gene knockout strains in 21 different environments. Ohya et al. (2005) report significant effects of 2059 haploid knockout strains on 254 morphological traits. Literature-curated phenotypic effects (physiological) and functional categories of yeast genes are reported in the Comprehensive Yeast Genome Database (CYGD) (http://mips.helmholtz-muenchen.de/genre/proj/yeast/). Further gene functional annotation is provided by the Gene Ontology (GO) database (http://www.geneontology.org/), accessed on August 16, 2012, where pleiotropy is assessed by counting the number of (nonredundant) GO categories associated with each gene, considering three main functional categories or their union. Genome-wide gene expression levels are provided by Holstege et al. (1998) for 5449 yeast genes. We assessed the correlation between the log-transformed expression level and pleiotropic degree using Spearman’s rank correlation (r_Spearman) and Pearson’s (r_Pearson) estimates. Because of a lack of normality, significance was assessed by randomization, permuting the pleiotropic degree among genes randomly 10,000 times. We report the two-tailed P-values (P). n_genes reports the number of genes present in both the pleiotropy and gene expression data set, and n_traits is the total number of traits affected by the genes in each analysis. All significant correlations are positive.