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.

Evans BMC Genomics 2010 11:286   doi:10.1186/1471-2164-11-286

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