Table 1.

Cross-platform comparison of genes called up and down.

Cross	Affymetrix	Agilent	overlap	% agreement	% transcription factors
2x X 4x up	597	755	157	26.3	12.1
2x X 4x down	818	378	93	24.6	14
2x X 6x up	821	814	288	35.4	10.8
2x X 6x down	877	1072	392	44.7	13.6
4x X 2x up	1164	870	300	34.5	7.3
4x X 2x down	1854	801	326	40.7	8.6
6x X 2x up	1388	2109	776	55.9	9.7
6x X 2x down	1859	2333	921	49.5	7.5
fis1 X 2x up	1068	2582	401	37.5	10.5
fis1 X 2x down	1904	3039	710	37.3	11.3
msi1 up	1691				10.2
msi1 down	2414				7.6

The numbers of genes called up or down for each cross and each platform are shown, along with the numbers of genes in common across both platforms for each cross ('overlap'), and the percentage of the maximum possible agreement between platforms. The right-hand column shows the percentage of each list consisting of transcription factors (http://datf.cbi.pku.edu.cn; Guo et al., 2005). For all samples except for msi1 the percentage of transcription factors was calculated from the lists of genes called up or down in both platforms ('overlap'). See Additional file 2 table S2 for genes called up or down in each platform and Additional file 3 table S3 for genes called up or down in both platforms.