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

BMC Genomics

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

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

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.

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