Comparison of Sox6 binding and Pol II binding to the Sox6 target genes. Left Y axis shows fold enrichment of Sox6 obtained by the peak calling program SISSRs using the 3 million read data set (see the text for detail), and right Y axis shows Pol II binding levels to the Sox6 peak-associated genes measured in RPKM. X axis shows all Sox6-associated genes (867 RefSeq genes in total) sorted according to Pol II binding and chromosomal location. When multiple Sox6 peaks were associated with one gene, only the peak with the highest fold enrichment was used. Note that Pol II binding to β-actin, an abundantly expressed housekeeping gene, was 8.60 RPKM. A similar result was obtained using the 1.5 million read-data set (data not shown).