Systematic identification of yeast cell cycle transcription factors using multiple data sources

BMC Bioinformatics

Table 1 The 17 identified cell cycle TFs

TF name	Hypergeometric p-value	MG₁	G₁	S	SG₂	G₂M
Fkh2	< 10^-11		C [12, 13]		E [3, 7]	E [21, 22]
Mbp1	< 10^-11		E [3, 19]	C [12, 13]
Mcm1	< 10^-11	E [17, 18]		C [12]		E [21, 22]
Swi4	< 10^-11	C [2, 12, 13, 26]	E [3, 19]	E [7, 20]		C [12, 13]
Swi6	< 10^-11		E [3, 19]		E [3, 7]
Tec1	1.8 × 10^-11	C [2, 12, 13]	C [13]			C [12]
Ndd1	3.5 × 10^-11		C [12, 13]			E [21, 22]
Ash1	9.6 × 10^-10	C [2]	C [14]
Ste12	2.2 × 10^-9	C [12, 13, 26]	C [13, 26]			N
Swi5	6.2 × 10^-9	E [16]
Fkh1	6.9 × 10^-9				E [3, 7]	E [21, 22]
Rlm1	2.1 × 10^-7	C [13]	C [13]	N
Stb1	1.3 × 10^-6		C [2, 13, 26]
Stp1	4.7 × 10^-5					N
Ace2	1.2 × 10^-4	E [16]
Cin5	1.8 × 10^-4					C [13]
Cst6	3.5 × 10^-4	N				N

The twelve known cell cycle TFs (according to the MIPS database) are bold-faced and colored blue. The 17 identified TFs are ordered by the confidence of being cell cycle TFs (according to the hypergeometric p-value calculated using Equation (4)). For each identified cell cycle TF, the cell cycle phases in which the TF functions are shown. "E" means that the prediction is supported by experimental evidence, "C" means that the prediction is supported by previous computational studies, and "N" stands for our novel prediction.

ISSN: 1471-2105