Exploratory differential gene expression analysis in microarray experiments with no or limited replication

Table 4 Comparison of genes identified as differentially expressed in mac1Δ

Gene	ORF	Loguinov et al. (this work) (0.0001)	Hughes et al. [18] (0.0001)	Churchill and Sapir [20] (0.9999)	Newton et al. [19] (0.9999)	2FC	Reference
*FTH1*	*YBR207W*	+	+	+	+	+	[67]
*PCA1*	*YBR295W*	+	a	+	+	a	[68]
*AKR1*	*YDR264C*	+	a	+	+	a	[69]
*CCC2*	*YDR270W*	+	+	+	+	+	[67]
*FIT1*	*YDR534C*	+	a	+	+	+	[70]
*SIT1*	*YEL065W*	+	+	+	+	+	[70]
*FTR1*	*YER145C*	+	+	+	+	+	[67]
*FET5*	*YFL041W*	+	a	+	+		[71]
	YFR055W*	-	b	b	b	b	[72]
*CTT1*	YGR088W*	-	b	b	b	b	[33]
*VMR1*	*YHL035C*	+	+	+	+	+	[69]
*ARN1*	*YHL040C*	+	+	+	+	+	[70]
*ARN2*	*YHL047C*	+	+	+	+	+	[70]
*FRE2*	*YKL220C*	+	a	+	+	+	[67]
*MRS4*	YKR052C*	+	a	a	a	a	[73]
*FRE6*	*YLL051C*	+	a	+	+	a	[74]
*SMF3*	YLR034C*	+	a	a	a	a	[75]
*TIS11*	*YLR136C*	+	a	+	+	a	[76]
*HMX1*	*YLR205C*	+	+	+	+	+	[77]
*FRE1*	*YLR214W*	+	+	+	+	+	[67]
*MAC1*	*YMR021C*	-	a	-	-	-	[33]
*FET3*	*YMR058W*	+	+	+	+	+	[67]
*ATX1*	*YNL259C*	+	a	+	+	a	[78]
*BIO5*	*YNR056C*	+	a	+	+	+	[69]
*FRE4*	*YNR060W*	+	a	+	+	+	[74]
*ARN4*	*YOL158C*	+	+	+	+	+	[70]
*FRE3*	*YOR381W*	+	+	+	+	+	[74]
*FIT2*	*YOR382W*	+	+	+	+	+	[79]
*FIT3*	*YOR383C*	+	+	+	+	+	[79]
*FRE5*	*YOR384W*	+	+	+	+	+	[74]

The performance of each method (except Chen et al. [17]) at equivalently high stringency levels is presented for selected genes likely to be differentially expressed in mac1Δ as described in text. For Sapir and Churchill [20], the cut-off (0.9999) corresponds to posterior probability of being differentially expressed and for Newton et al. [19], the cut-off 0.9999 is posterior probability of true differential expression. For this work, 0.0001 is a cut-off for q-values. For Hughes et al. [18], 0.0001 is a cut-off for p-values. 2FC is indicates two-fold change approach. A (+) sign indicates that a gene was identified as up-regulated by a method at this level of stringency while a (-) sign indicates that it was identified as down-regulated. Genes not identified by one method that were identified by other methods are indicated by a (+) or b (-) in the appropriate column. Genes identified only by this work are asterisked.

ISSN: 1474-760X