Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments

Table 1 Pairwise comparisons of gene-expression level category by mean log₂ ratio and by Bayesian estimation with statistical significance

Strain	Environment	Category*	Mean log₂ ratio	Significant^†	Not significant	Total
S288C	Ethanol shocked	> 2-fold	2,235	87	1,523	1,610
S288C	versus mid-log growth	< 2-fold	3,504	0	2,767	2,767
		Excluded	399		1,761	6,138
swi1Δ and snf2Δ	Rich medium	> 2-fold	114	170	46	216
versus S288C	Rich medium	< 2-fold	5,987	81	5,704	5,785
		Excluded	41		141	6,142
swi1Δ and snf2Δ	Minimal medium	> 2-fold	218	243	14	257
versus S288C	Minimal medium	< 2-fold	5,883	361	4,890	5,251
		Excluded	41		634	6,142
DY1457 versus	Zinc-limited	> 2-fold	1,034	419	471	890
DY1457	versus zinc-replete	< 2-fold	5,118	309	4,953	5,262
		Excluded	0		0	6,152
DY1457 versus	Zinc-limited	> 2-fold	678	198	310	508
DY1457 zap1	Zinc-limited	< 2-fold	5,474	122	5,522	5,644
		Excluded	0		0	6,152

*Genes were excluded by necessity because of poor quality or insufficient replication of measurement. ^†Numbers are not corrected for multiple tests.

ISSN: 1474-760X