Table 2

Identifying regulatory roles of TFs. MOFA can determine the regulatory role of a TF in regulating genes of a module.

TF

Phase (Module Number)

Regulatory Role

P-value

Evidence from Literature

Abf1

S/G2 (4)

Activator

6 × 10-5

[40]

Abf1

G1 (23)

Repressor

0.001

[41]

Fkh1

S/G2 (1); G2/M (1)

Activator

3 × 10-8; 1 × 10-7

[37]

Fkh1

G1 (3)

Repressor

3 × 10-5

[42]

Fkh2

S/G2 (1) (2) (3) ; G2/M (1) (3) (4) (5) (7) (13)

Activator

3 × 10-8; 3 × 10-7; 3 × 10-5; 1 × 10-7; 6 × 10-9; 3 × 10-5; 9 × 10-5; 6 × 10-9; 3 × 10-5

[37]

Fkh2

G1 (3)

Repressor

3 × 10-5

[42]

Reb1

G2/M (18)

Activator

2 × 10-4

[43]

Reb1

G1 (30)

Repressor

2 × 10-5

[44-46]

Ace2

M/G1 (2)

Activator

9 × 10-5

[28,47]

Ndd1

S/G2 (2); G2/M (1) (7)

Activator

3 × 10-5; 1 × 10-7; 6 × 10-6

[48,49]

Stb1

G1 (33)

Activator

2 × 10-11

[33,50]

Swi4

G1 (13) (22) (34)

Activator

6 × 10-9; 1 × 10-6; 2 × 10-4

[51]

Swi5

M/G1 (13)

Activator

6 × 10-8

[28,47]

Dat1

M/G1 (1); G1 (1) (7)

Repressor

3 × 10-5; 3 × 10-7; 3 × 10-5

[52]

Yox1

M/G1 (15)

Repressor

3 × 10-7

[30]

A TF is said to be an activator/repressor of a module if the P-value of observing TF-gene pairs of the module having positively/negatively (time-shifted) correlated profiles is ≤ 0.001. The P-value is the probability that an observation would be made by chance, and is calculated using the cumulative binomial distribution [39]:

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/421/mathml/M1','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/421/mathml/M1">View MathML</a>

where N is the total number of genes in a module, n0 is the number of genes that have temporal relationships with the TF, and p is the probability of observing an arbitrary gene in the genome that has a temporal relationship with the TF.

Wu et al. BMC Bioinformatics 2006 7:421   doi:10.1186/1471-2105-7-421

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