Table 1.

Number of differentially expressed genes. Numbers of identified differentially expressed genes in the GP and GOT models after preprocessing by 0 or more MIDAS pipeline steps — IIV, IIV_T, IIV_TL, IIV_TLS, or IIV_TSLF. For Experiment 1, up-expression (+) and down-expression (-) numbers are given for both WT and antiPLD. For Experiment 2, + and -1 numbers are given for all 4 genotypes separately. The ALL entries correspond to the H1 hypotheses of the GOT model (see Materials and Methods).

Genotype		IIV	IIVT	IIVTL	IIVTLS	IIVTLSF
		GP Model — Experiment 1
WT	+	567	571	487	495	460
WT	-	552	553	499	499	460
antiPLD	+	442	421	440	471	431
antiPLD	-	336	346	381	363	334
		GOT Model — Experiment 2
Col-0	+	227	309	242	240	270
Col-0	-	122	171	178	180	183
Cvi-0	+	106	108	82	78	71
Cvi-0	-	63	93	74	71	67
WS	+	234	346	279	269	150
WS	-	331	347	340	340	224
Th	+	238	398	350	363	361
Th	-	196	245	241	246	240
ALL	+	298	428	357	354	290
ALL	-	202	261	253	248	195