Table 3. Distribution of induced and repressed genes among lineage specificity cohorts and chromosomal locations.

	Number of genes	Differentially expressed	UP' (observed)	DOWN' (observed)	UP' (expected)	DOWN' (expected)	χ2	p
Aspergillus core	5095	965	414	551	482.5	482.5	19.45	<0.0001
Affc-core	6907	1468	791	677	734	734	8.853	0.0029
Affc-specific	180	64*	54	10	32	32	30.25	<0.0001
Afu-specific	428	135*	77	58	67.5	67.5	2.674	0.102

Chi-square analysis (with one degree of freedom) was used to test the distribution of induced and repressed genes with respect to lineage specificity and sub-genomic locations, based upon the null hypothesis that equal numbers of induced and repressed genes occur in each cohort. Asterisked gene populations are listed in Supplementary Table S5.