Table 1.
Highest scoring motifs detected by REDUCE analysis
| Motif
|
R2
|
P value
|
F
|
Matches
|
Loci
|
Consensus
|
|---|---|---|---|---|---|---|
| A dMnt | ||||||
| CGCG | 0.051 | 0.0E + 00 | 0.01 | 66,217 | 4366 | CG-repeat |
| GCGC | 0.048 | 0.0E + 00 | 0.01 | 97,925 | 4367 | CG-repeat |
| CGCGC | 0.047 | 0.0E + 00 | 0.02 | 16,661 | 4121 | CG-repeat |
| GCGCG | 0.042 | 0.0E + 00 | 0.02 | 17,392 | 4129 | CG-repeat |
| TATCGATA | 0.026 | 0.0E + 00 | 0.06 | 1618 | 1258 | TATCGATA |
| ATCGATA | 0.024 | 0.0E + 00 | 0.04 | 3863 | 2367 | TATCGATA |
| TCGATA | 0.015 | 1.0E − 12 | 0.02 | 8262 | 3541 | TATCGATA |
| TATCGAT | 0.015 | 5.0E − 12 | 0.03 | 3765 | 2369 | TATCGATA |
| GGTCACAC | 0.024 | 0.0E + 00 | 0.09 | 788 | 706 | GGTCACACT |
| GTCACACT | 0.017 | 0.0E + 00 | 0.08 | 691 | 633 | GGTCACACT |
| CACGTG | 0.019 | 0.0E + 00 | 0.03 | 4214 | 2558 | CACGTG |
| GCACGTG | 0.016 | 0.0E + 00 | 0.05 | 1370 | 1139 | CACGTG |
| GCACGTGT | 0.012 | 9.8E − 09 | 0.10 | 319 | 301 | CACGTG |
| B dMax | ||||||
| CGCGC | 0.025 | 0.0E + 00 | 0.02 | 16,401 | 4058 | CG-repeat |
| CGCG | 0.022 | 0.0E + 00 | 0.01 | 65,098 | 4301 | CG-repeat |
| GCGCG | 0.020 | 0.0E + 00 | 0.02 | 17,086 | 4069 | CG-repeat |
| GCGC | 0.014 | 2.0E − 12 | 0.00 | 96,364 | 4302 | CG-repeat |
| TATCGATA | 0.024 | 0.0E + 00 | 0.07 | 1600 | 1247 | TATCGATA |
| ATCGATA | 0.018 | 0.0E + 00 | 0.04 | 3797 | 2330 | TATCGATA |
| TATCGAT | 0.016 | 2.0E − 12 | 0.04 | 3705 | 2334 | TATCGATA |
| GGTCACAC | 0.013 | 2.0E − 09 | 0.08 | 776 | 693 | GGTCACACT |
| GTCACACT | 0.009 | 1.1E − 05 | 0.07 | 681 | 624 | GGTCACACT |
| C dMyc (high dMax) | ||||||
| CACGTG | 0.032 | 0.0E + 00 | 0.03 | 4203 | 2555 | CACGTG |
| ACGTG | 0.024 | 0.0E + 00 | 0.01 | 18,323 | 4228 | CACGTG |
| CACGT | 0.022 | 0.0E + 00 | 0.01 | 17,082 | 4221 | CACGTG |
| GCACGTG | 0.021 | 0.0E + 00 | 0.05 | 1365 | 1134 | CACGTG |
| ATCGATA | 0.022 | 0.0E + 00 | 0.03 | 3853 | 2362 | TATCGATA |
| TCGATA | 0.022 | 0.0E + 00 | 0.02 | 8255 | 3535 | TATCGATA |
| TATCGATA | 0.020 | 0.0E + 00 | 0.04 | 1616 | 1256 | TATCGATA |
| ATCGAT | 0.014 | 2.2E − 11 | 0.01 | 13,336 | 4037 | TATCGATA |
| TATCGAT | 0.013 | 2.1E − 10 | 0.02 | 3751 | 2362 | TATCGATA |
| CGCGC | 0.027 | 0.0E + 00 | 0.01 | 16,646 | 4116 | CG-repeat |
| CGCG | 0.026 | 0.0E + 00 | 0.00 | 66,118 | 4361 | CG-repeat |
| GCGC | 0.024 | 0.0E + 00 | 0.00 | 97,752 | 4362 | CG-repeat |
| GCGCG | 0.019 | 0.0E + 00 | 0.01 | 17,348 | 4124 | CG-repeat |
For each spot on the microarray the Berkeley Drosophila Genome Sequence Release 2 was used to generate an associated DNA region comprising the sequence of the array probe plus 2 kb flanking region. The Matches column indicates the total number of matches to the motif in the combined sequences. The Loci column indicates the number of sequences with at least one match. F represents the regression coefficient for a given motif. R2 equals the square of the Pearson correlation between the binding log ratio and the motif count (see Materials and Methods). All oligonucleotides of up to 8 bp in length were tested in parallel. Only the most significant motifs (p < 10−4) with a positive correlation are shown. E-box and DRE sequences are depicted in bold. Complete REDUCE results available in Supplemental Material S5.