TABLE 1.

The number of genes significant for parental expression difference, cis effect, trans effect, or imprinting effect at different thresholds

	Difference between parents					cis effect
Deltaa	Sig+b	Sig−b	Total	False	FDR (%)	Sig+b	Sig−b	Total	False	FDR (%)
0.15	8962	1286	10248	4330	42	5098	3196	8294	3577	43
0.25	8066	1004	9070	1394	15	3839	2274	6113	543	8.9
0.35	7046	695	7741	256	3.3	2800	1618	4418	81	1.8
0.45	5799	501	6300	48	0.77	2002	1183	3185	25	0.80
0.55	4644	360	5004	13	0.25	1500	825	2325	11	0.46
0.65	3558	253	3811	4	0.11	1075	590	1665	5	0.30
0.75	2606	200	2806	1	0.048	773	453	1226	3	0.20
0.85	1657	165	1822	1	0.032	558	344	902	1	0.15
0.95	1077	127	1204	0	0.024	408	265	673	1	0.094
	trans effect					Imprinting effect
Deltaa	Sig+b	Sig−b	Total	False	FDR (%)	Sig+b	Sig−b	Total	False	FDR
0.15	45	10018	10063	4627	46	11	0	11	2895	26317
0.25	12	8121	8133	1542	19	4	0	4	295	7379
0.35	6	6326	6332	302	4.8	3	0	3	8	282
0.45	5	4422	4427	47	1.1	3	0	3	1	37
0.55	3	2907	2910	11	0.37	0	0	0	0	NA
0.65	3	1685	1688	2	0.15	0	0	0	0	NA
0.75	3	729	732	1	0.080	0	0	0	0	NA
0.85	3	248	251	0	0.085	0	0	0	0	NA
0.95	2	91	93	0	0.080	0	0	0	0	NA

FDR was determined on the basis of 1000 permutations for 12,311 analyzed genes. Note that some FDR was >100%. This was due to the d score distribution of nonsignificant genes in real data being tighter than the null (Tusher et al. 2001), meaning no significant enrichment over background. Boldface highlights the number of significant genes described in the main text.

^aDelta, the thresholds.

^bSig+ and Sig−, the number of genes significant for each of the two directions of comparison. For parental expression difference, + indicates that expression level is greater in Col; for cis effect, + indicates that cis variation upregulates Col; for trans effect, + indicates that trans variation upregulates Van; for imprinting effect, + indicates that Col allele is upregulated in Col-mother F₁ hybrids.