Supplementary Information to "Nucleotides of Transcription Factor Binding Sites Exert Interdependent Effects on the Binding Affinities of Transcription Factors"

(Martha L. Bulyk, Philip L. F. Johnson, George M. Church)

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Web Table 1

Correlation coefficients between four types of interdependence control datasets - all mononucleotide (1NN x N2N x NN3), first dinucleotide (12N x NN3), second dinucleotide (1NN x N23), and trinucleotide (123) – and values calculated by all three of our methods. The first type of control had mononucleotide interdependence generated by making a random mononucleotide weight matrix and multiplying the entries (1NN x N2N x NN3) to calculate the K_a^app for each triplet. The second type of control depended on the first dinucleotide (12N) and the third mononucleotide (NN3); it was created from a random matrix with one column of dinucleotides and another of mononucleotides. Again, the entries were multiplied (12N x NN3) to yield the K_a^app’s. The third type depended on the first mononucleotide (1NN) and the second dinucleotide (N23) and was created using the same method (1NN x N23). The fourth type of control (123) exhibited interdependence at the triplet level.Each triplet was assigned a random number, and then these numbers were normalized such that the sum of the 64 triplets would equal one. Coefficients represent mean values over 1000 sets of independent random controls.

Control type	1*2*3	12*3	1*23
1NNxN2NxNN3	1.00	1.00	1.00
12NxNN3	0.782	1.00	0.782
1NNxN23	0.780	0.780	1.00
123	0.370	0.529	0.527