TABLE 2

Over- and underrepresented oligonucleotides found in the flanking regions of AhR sites

The first nine characteristics are `positive' and the last four are `negative'. The sequences considered were of the length 111 bp (11-bp AhR site in the center and 50-bp flanks).

Oligonucleotidea From Tob In/Outc Utilityd FreqYe FreqNf FreqY/FreqNg
RDVB 0 15 0 0.60 3.333333 2.313131 1.441048
CNYK 36 71 0 0.84 3.333333 2.121212 1.571429
DYSY 33 87 0 0.68 8.037037 5.717172 1.405771
YRMG 9 57 0 0.61 2.000000 0.838384 2.385542
SVWY 30 42 0 0.56 0.962963 0.252525 3.813334
SBDY 33 39 0 0.73 1.037037 0.171717 6.039216
WHRH 51 63 0 0.69 1.000000 0.222222 4.500000
THDM 48 66 0 0.69 0.888889 0.232323 3.826087
DYVC 58 68 1 0.77 9.407408 6.282828 1.497321
WANW 12 87 0 0.61 1.370370 4.262626 0.321485
WBNR 48 52 0 0.60 0.000000 0.555556 0.000000
HBWG 48 52 0 0.60 0.000000 0.505050 0.000000
CVD 61 62 0 0.60 0.074074 0.565657 0.130952

  • ↵ a The oligonucleotide over- or underrepresented in the sequences (written in the ambiguous one-letter code).

  • ↵ b Positions of the window.

  • ↵ c Oligonucleotides are counted in the window (0) or outside the window (1).

  • ↵ d Utility = utility value U (−1 < U < 1) is an indicator of significance of the difference between two distributions of frequencies freqY and freqN. Utility is calculated on the bases of a number of statistical criteria including tests of mean difference, distribution overlapping, normal-likeness, and bootstrap tests.

  • ↵ e FreqY, frequency of the oligonucleotide in the AhR site sequences (average number of oligonucleotides in the window).

  • ↵ f FreqN, frequency of the olig in the background sequences.

  • ↵ g FreqY/FreqN, relative frequency in Y vs. N.