Table 1. Significant cooperative TF pairs of cell cycle target genes. The TF pairs are sorted by value.

Ranking	TF1	TF2	PC ^*	Literature evidences
1	Swi4	Swi6	2.68E-162	Kumar et al.; Koch et al.; Manke et al.; Banerjee and Zhang; Tsai et al.^a
2	Mbp1	Swi6	7.32E-125	Koch et al.; Manke et al.; Banerjee and Zhang; Tsai et al.^a
3	Fkh2	Ndd1	1.55E-88	Koranda et al.; Manke et al.; Banerjee and Zhang; Tsai et al.^a
4	Mbp1	Swi4	4.07E-83	Koch et al.; Manke et al.
5	Gat3	Yap5	1.40E-76	Manke et al.
6	Fkh2	Swi6	7.30E-59	Tsai et al.^a
7	Fkh1	Fkh2	7.25E-58	Kumar et al.; Zhu et al.; Pic et al.; Manke et al.; Banerjee and Zhang
8	Pdr1	Yap5	2.69E-49	Manke et al.
9	Fkh2	Swi4	1.00E-48	Manke et al.; Tsai et al.^a
10	Mcm1	Ndd1	2.46E-46	Kumar et al.; Koranda et al.; Manke et al.; Banerjee and Zhang; Tsai et al.^a
11	Fkh2	Mbp1	8.94E-46	Manke et al.; Tsai et al.^b
12	Fkh1	Swi6	4.00E-45
13	Gat3	Pdr1	3.42E-44	Manke et al.; Banerjee and Zhang; Tsai et al.^b
14	Fkh1	Ndd1	8.97E-43	Koranda et al.; Banerjee and Zhang; Tsai et al.^a
15	Ndd1	Swi6	1.00E-42
16	Msn4	Yap5	1.76E-41	Banerjee and Zhang; Tsai et al.^b
17	Gat3	Msn4	1.00E-39	Banerjee and Zhang; Tsai et al.^b
18	Fkh2	Mcm1	1.41E-39	Kumar et al.; Pic et al.; Manke et al.; Banerjee and Zhang; Tsai et al.^b
19	Stb1	Swi6	1.58E-38	Ho et al.; Costanzo et al.
20	Cin5	Yap6	2.21E-37	Manke et al.; Banerjee and Zhang
21	Ndd1	Swi4	7.19E-37	Manke et al.; Tsai et al.^a
22	Gat3	Hap4	1.00E-36
23	Hap4	Yap5	1.00E-36	Tsai et al.^b
24	Fkh1	Mbp1	1.95E-36	Tsai et al.^a
25	Stb1	Swi4	4.80E-35	Costanzo et al.; Manke et al.; Banerjee and Zhang; Tsai et al.^b
26	Ste12	Swi6	1.54E-34
27	Ste12	Swi4	3.06E-34
28	Gat3	Rap1	2.27E-33
29	Msn4	Pdr1	6.00E-33	Tsai et al.^b
30	Rap1	Yap5	6.34E-33
31	Dig1	Ste12	2.28E-32	Olson et al.; Manke et al.; Tsai et al.^b
32	Mbp1	Ndd1	4.90E-32	Manke et al.
33	Dat1	Yap5	1.85E-31
34	Ace2	Swi5	7.77E-31	Doolin et al.; Manke et al.; Banerjee and Zhang
35	Skn7	Swi6	1.61E-29
36	Dat1	Gat3	1.00E-27
37	Dat1	Hap1	1.00E-27	Tsai et al.^a
38	Dat1	Hap4	1.00E-27
39	Rlm1	Swi4	1.00E-27
40	Rlm1	Swi6	1.00E-27
41	Mcm1	Swi6	1.94E-27
42	Fkh1	Mcm1	6.80E-26	Kumar et al.; Tsai et al.^b
43	Mbp1	Stb1	9.80E-26	Costanzo et al.
44	Skn7	Swi4	1.99E-25	Manke et al.
45	Gat3	Rgm1	1.00E-24	Manke et al.
46	Pdr1	Rgm1	1.00E-24	Manke et al.
47	Hap1	Msn4	2.00E-24	Tsai et al.^b
48	Hap4	Pdr1	3.00E-24	Tsai et al.^b
49	Pdr1	Smp1	3.00E-24	Manke et al.; Banerjee and Zhang
50	Dat1	Msn4	4.00E-24	Tsai et al.^b
51	Hap1	Rap1	9.50E-23	Tsai et al.^a
52	Hap1	Yap5	2.40E-22	Tsai et al.^b
53	Rgm1	Yap5	3.41E-22	Manke et al.
54	Swi5	Yap5	3.60E-22	Tsai et al.^b
55	Hap1	Hap4	5.66E-22

^* List of the results with smaller than =10^-21.

^a Confident synergistic TF pairs as stated in Tsai et al.’s study (2005).

^b Plausible or doubtful synergistic TF pairs as stated in Tsai et al.’s study (2005).