Table 3.

Comparison of MIV and IIV. We compare MIV and IIV input data with respect to the sets of genes ultimately identified as differentially expressed. The genotype and set labelings are the same as those in Table 1. The GP model was used to analyze the unnormalized MIV and IIV data from Experiment 1. The GOT model was used to analyze the unnormalized MIV and IIV data from Experiment 2. Up-expressed and down-expressed counts are reported for both experiments and all genotypes. The count of genes in the intersections is found in column Common. For convenience, percentages of the intersection with respect to the MIV and IIV sets are tabulated in the last two columns. The ALL entries correspond to the H1 hypotheses of the GOT model (see Materials and Methods).

Genotype		MIV	IIV	Common	% of common in MIV	% of common in IIV
		GP Model — Experiment 1
WT	+	725	567	501	69.10%	88.36%
WT	-	774	552	515	66.54%	93.30%
antiPLD	+	518	422	357	68.92%	84.60%
antiPLD	-	505	336	313	61.98%	93.15%
		GOT Model — Experiment 2
Col-0	+	311	227	198	63.67%	87.22%
Col-0	-	190	122	110	57.89%	90.16%
Cvi-0	+	185	106	89	48.11%	83.96%
Cvi-0	-	97	63	59	60.82%	93.65%
ws	+	326	234	181	55.52%	77.35%
ws	-	482	331	273	56.64%	82.48%
Th	+	363	238	219	60.33%	92.02%
Th	-	251	196	166	66.14%	84.69%
ALL	+	448	298	249	55.58%	83.56%
ALL	-	294	202	159	54.08%	78.71%