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Table 1 Five existing TFBS-based RS measures

From: A regulatory similarity measure using the location information of transcription factor binding sites in Saccharomyces cerevisiae

RS measure Equation
Garten et al.1 - log x k min ( m , n ) m x N - m n - x N n Eq. (1)
Veerla and Höglund T F a T F b T F a T F b Eq. (2)
Shalgi et al. T F a T F b min T F a , T F b Eq. (3)
Park et al.2 S = j = 1 2 γ j i f i j - 1 / 2 2 N 1 i j + N 2 i j + α C i j - β N 1 i j + N 2 i j I C i j = 0 Eq. (4)
van Helden2 M a b = S a b - α D a b + β Eq. (5)
  1. RS measures of two genes, a and b. TF a and TF b represent the TFs whose TFBSs exist in the promoter of a and b, respectively. 1In Eq. (1), N is the number of TFs whose binding sites are in the collected TFBS data, m=|TF a |, n=|TF b | and k=|TF a TF b |. 2Equations (4) and (5) only show the final equations of the two works. The equation details can be found in the original manuscripts [7, 8].