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Table 4 Proportion of binding sites in the preferred classes for regions of low tag density in the control library

From: Most transcription factor binding sites are in a few mosaic classes of the human genome

Factor Number TFBS Number TFBS Ratio (3)/(2) Proportion in preferred classes Proportion in preferred classes
  All Low tag   All Low tag
1 2 3 4 5 6
GATA1 3367 1681 0.499 0.736 0.703
TR4 541 247 0.457 0.870 0.860
ZNF263 5098 3297 0.647 0.856 0.835
cFos 3746 1834 0.490 0.603 0.561
Max 3176 1382 0.435 0.675 0.614
NF-E2 4700 2322 0.494 0.536 0.489
Average of above    0.504 0.713 0.677
  1. Column 2 gives the number of sites and column 5 the proportion of TFBSs in the preferred classes for all TFBS (as in columns 4 and 9 of Table 2). Columns 3 and 6 give this information for regions of low tag density in the control library, "sparse regions". Column 4 gives the proportion of sites in these regions. Note that the final column is very close to the preceding column and that often a substantial fraction of TFBSs are in "sparse regions". We conclude that the final results are not affected by experimental bias reflected in the control library. This analysis has been done for the "YALE" experiments using cell lines K562 and K562b. For K562, "sparse regions' were defined as a tag density of 0 or 1 in the input signal, and for K562b as a tag density of 0, 1 or 2.