. 2008 Mar 20;9(Suppl 1):S20. doi: 10.1186/1471-2164-9-S1-S20

Table 2.

Whole genome ER ChIP-chip results based on either Affymetrix or xMAN probe mapping under different FDR thresholds

FDR thresholds (%)	0	1	2	5
Affymetrix^a	2,646 (2,312)	5,221 (4,572)	5,714 (4,993)	7,293 (6,413)
xMAN^a	3,281 (2929)	6,544 (5,820)	7,563 (6,760)	8,890 (7,925)
Shared Regions^b	2,475 (2,217)	5,006 (4,481)	5,436 (4,876)	6,871 (6,184)
Percentage of Shared Regions^c	93.5 (95.9)	95.9 (98.0)	95.1 (97.6)	94.2 (96.5)

^aThe numbers of ChIP-regions identified by MAT are shown in the table. A ChIP-region is annotated as repeat if more than 70% of the region is within RepeatMasker repeats, simple repeats, or segmental duplications. The numbers of non-repeat regions are shown in the parentheses.

^bChIP-regions identified from Affymetrix_NCBIv34 probe mapping were converted into NCBIv35 version using LiftOver program (http://genome.ucsc.edu/cgi-bin/hgLiftOver). Two regions are considered the same if they overlap by more than 50%.

^cThe percentage of shared regions was defined as the number of shared regions divided by the number of regions identified using Affymetrix probe mapping.