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Table 2 Whole genome ER ChIP-chip results based on either Affymetrix or xMAN probe mapping under different FDR thresholds

From: xMAN: extreme MApping of OligoNucleotides

FDR thresholds (%) 0 1 2 5
Affymetrixa 2,646 (2,312) 5,221 (4,572) 5,714 (4,993) 7,293 (6,413)
xMANa 3,281 (2929) 6,544 (5,820) 7,563 (6,760) 8,890 (7,925)
Shared Regionsb 2,475 (2,217) 5,006 (4,481) 5,436 (4,876) 6,871 (6,184)
Percentage of Shared Regionsc 93.5 (95.9) 95.9 (98.0) 95.1 (97.6) 94.2 (96.5)
  1. 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.
  2. 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%.
  3. cThe percentage of shared regions was defined as the number of shared regions divided by the number of regions identified using Affymetrix probe mapping.
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