Table 1.

Counts of QTLs are shown for each of the available transforms; the hippocampal BXD data set described in this report, the INIA whole brain expression data set which used 39 BXD strains (the smaller number of strains used in this study reflected in the lower cis-QTL counts), and another hippocampus data set using the LXS RI panel consisting of 75 strains. The two BXD data sets were created using Affymetrix chips and were normalized using the position-dependent nearest-neighbor (PDNN), Robust Multi-chip Average (RMA) or, in the case of the BXD Hippocampus data set, Affymetrix MAS5 algorithms, whereas the LXS data shown were processed using Illumina Sentrix Mouse-6 v 1.0 BeadArray technology and were normalized using the Loess (LOESS), Quantile (QUANT), or Rank Invariant (RankInv) methods. Values are given for the total number of QTLs, the number of cis-QTLs (marker within 5 Mb either side of the position of the gene encoding the transcript), or the number of trans-QTLs (marker outside a 10 Mb window surrounding the position of the gene encoding the transcript). The small discrepancy observed (cis-QTLs + trans-QTL < total QTL count) is due to those QTLs at exactly 5 Mb from the gene, and thus not classed as either cis or trans by this scan. Linkage maps were generated using 1000 permutation tests and a genome-wide significance score calculated. For the data shown, only QTLs are shown that were significant after genome-wide permutation testing at P ≤ 0.05 (normal typeface) or P ≤ 0.001 (italics).

		total QTLs	cis-QTLs	trans-QTLs
BXD	PDNN	5534/1496	2441/1244	2833/202
Hippocampus (June 2006)	RMA	5472/1464	2432/1237	2758/174
	MAS5	5253/1314	2193/1118	2807/158
BXD	PDNN	5580/1213	1999/1001	3248/158
Whole brain (January 2006)	RMA	5037/977	1072/827	3034/109
LXS	LOESS	2528/631	1096/553	1277/48
Hippocampus (August 2007)	QUANT	3244/675	1171/576	1871/61
	RankInv (May 2007)	3069/617	1117/531	1775/55