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Table 1 Cross-platform comparison of genes called up and down.

From: Transcriptional profiles underlying parent-of-origin effects in seeds of Arabidopsis thaliana

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
  1. 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.