Table 4

Replacing regulatory coupling strength by response to transcription factor deletion.

Transcription Factor

Number of genes in each group

GO category

B-

B+/D+

B+/D-

Not available

B+/D+

B+/D-

Dig1

5881

1

30

115

32

16

Gcn4

5928

16

63

60

19

17

Hir2

5941

2

19

105

24

5

Mbp1

5647

2

103

315

22

12

Swi4

5535

19

106

407

9

6

Swi5

5368

10

82

607

2

0

Yap1

5968

7

37

55

0

0

We analyzed the performance of a scheme in which our TF-gene coupling factor was replaced by the change in mRNA abundance in response to transcription factor deletion as a predictor of true targets. Significant binding (B+) was defined as before, while a significant response to deletion (D+) required P < 10^-2. The number of significantly over-represented GO categories is listed for both the B+/D+ and the B+/D- gene groups. The results indicate that TF deletion data is less useful than our coupling factor for distinguishing functional target genes from non-functional ones.

Gao et al. BMC Bioinformatics 2004 5:31   doi:10.1186/1471-2105-5-31