# Table 1 Five existing TFBS-based RS measures

RS measure Equation
Garten et al.1 $-\mathsf{\text{log}}\left(\sum _{x\ge k}^{\mathsf{\text{min}}\left(m,n\right)}\frac{\left(\begin{array}{c}\hfill m\hfill \\ \hfill x\hfill \end{array}\right)\left(\begin{array}{c}\hfill N-m\hfill \\ \hfill n-x\hfill \end{array}\right)}{\left(\begin{array}{c}\hfill N\hfill \\ \hfill n\hfill \end{array}\right)}\right)$ Eq. (1)
Veerla and Höglund $\frac{\left|T{F}_{a}\cap T{F}_{b}\right|}{\left|T{F}_{a}\cup T{F}_{b}\right|}$ Eq. (2)
Shalgi et al. $\frac{\left|T{F}_{a}\cap T{F}_{b}\right|}{\mathsf{\text{min}}\left(\left|T{F}_{a}\right|,\left|T{F}_{b}\right|\right)}$ Eq. (3)
Park et al.2 $\begin{array}{cc}S\hfill & =\sum _{j=1}^{2}{\gamma }_{j}\sum _{i}{\left({f}_{i}^{j}\right)}^{-1/2}\hfill \\ \left[\left(\frac{2}{{N}_{1i}^{j}+{N}_{2i}^{j}}+\alpha \right){C}_{i}^{j}-\beta \left({N}_{1i}^{j}+{N}_{2i}^{j}\right){I}_{\left\{{C}_{i}^{j}=0\right\}}\right]\hfill \end{array}$ Eq. (4)
van Helden2 ${M}^{ab}={S}^{ab}-\alpha {D}^{ab}+\beta$ 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].