Table 1. Frequency distribution (per kilobase) of binding motifs for various transcription factors 519 sequences, each 1058 bp long, pulled down by ChIP using anti-Ubx antibodies were searched for the presence of binding motifs for various transcription factor binding sites with MATCH using the motifs listed in TRANSFAC database (for Ubx, we also used motifs reported by Noyes et al., 2008 and Mann et al., 2009) under minimize false positive criterion. Similar analysis was done for randomly selected 519 contigs, each 1058 bp long from the fly genome and for the entire non-coding region of the fly genome. It should be noted that while binding motif for Ubx is not significantly enriched in the pulled down sequences, binding motifs for certain transcription factors such as GAF and MAD are significantly enriched. Others, although are statistically enriched, are represented at very low frequencies in both experimental and background sequences. The p-value was calculated from the z-score by taking the difference of the frequency of a motif in the ChIP-identified regions and its mean frequency in a sufficiently large set of random regions from the Drosophila genome (each consisting of 519 sequences 1058 bps long with coding regions masked), divided by the standard deviation of the frequency values for the random regions.

Transcription factor	Sequences pulled down using anti-Ubx antibodies	Randomly selected sequences	Entire non-coding genome	Fold change in frequency	p-value
GAGA factor	0.7361	0.1989	0.2098	3.7020	<10−10
MAD	0.4281	0.2176	0.2163	1.9674	<10−10
Ubx (TRANSFAC)	0.4165	0.4533	0.4886	0.9188	0.1383
Ubx (Mann et al., 2009)	8.170	10.377	10.635	0.7873	<10−10
Ubx (Noyes et al., 2008)	1.147	1.479	1.557	0.7756	3.4×10−6
Adf-1	0.0910	0.0313	0.0320	2.9110	7.1×10−7
Grainyhead/Elf-1/NTF-1	0.0871	0.0385	0.0394	2.2648	2.6×10−8
DREF	0.0464	0.0235	0.0223	1.9787	0.0036
OVO	0.0387	0.0231	0.0228	1.6784	0.0207
Snail	0.0154	0.0088	0.0099	1.7563	0.0727
Su(H)	0.0038	0.0004	0.0005	8.6216	1.8×10−4
dTCF	0.0038	0.0006	0.0007	6.7526	0.0014