TABLE 1.

The number of genes with significant cis and trans eQTL in three data sets at different numbers of expected false positives

			E (false positives)
Data set	Type	Method	100	10	1
Yeast	cis	t-test	646	506	398
		SVA	817	617	490
		ICE	1118	935	757
	trans	t-test	1845	1067	738
		SVA	612	293	167
		ICE	539	363	263
BXD whole brain	cis	t-test	71	43	32
		SVA	148	79	42
		ICE	193	120	69
	trans	t-test	201	61	22
		SVA	82	11	5
		ICE	131	21	11
BXD HSC	cis	t-test	40	19	10
		SVA	28	14	12
		ICE	50	23	13
	trans	t-test	94	8	1
		SVA	102	11	1
		ICE	103	9	1

A total of 5534 genes are tested in the yeast data set, and 8596 genes are tested in the two BXD mouse data sets.