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Table 3 Functional enrichment in correctly predicted positive genes. Predefined motifs: the models built with predefined motifs. Auto motifs: the models built with auto motifs. Up: the models built for up-regulated genes. Down: the models built for down-regulated genes. #Gp: the number of Gp genes (positive genes that are predicted as positive by a model). #Gn: the number of Gn genes (positive genes that are predicted as negative by a model). : the number of enriched functional categories in the set of Gp genes. : the number of enriched functional categories in the set of Gn genes. : the number of enriched functional categories in the set of Gp' genes (see text). The sample sizes for up- and down-regulated genes in cell cycle are 56 and 59, respectively, and 167 and 164 in stress conditions. The ranges represent individual 95% confidence interval for the means.

From: CAGER: classification analysis of gene expression regulation using multiple information sources

Model

#Gp

#Gn

Predefined motifs

Cell cycle

Up

17.2 ± 2.2

27.1 ± 2.7

15.1 ± 2.9

8.2 ± 2.6

12.3 ± 3.5

  

Down

14.0 ± 2.1

31.0 ± 2.5

14.5 ± 3.7

9.6 ± 3.4

8.4 ± 3.3

 

Stress

Up

16.4 ± 1.0

33.1 ± 1.1

13.4 ± 2.3

10.6 ± 1.8

10.3 ± 1.9

  

Down

21.0 ± 2.0

30.7 ± 1.7

17.1 ± 2.4

7.8 ± 1.7

14.7 ± 2.3

Auto motifs

Cell cycle

Up

24.9 ± 1.8

19.3 ± 1.8

16.9 ± 3.2

7.9 ± 2.5

13.9 ± 3.2

  

Down

23.6 ± 1.9

21.4 ± 1.8

15.6 ± 3.7

8.4 ± 2.9

11.8 ± 3.5

 

Stress

Up

27.0 ± 0.8

22.6 ± 0.8

16.2 ± 2.3

9.1 ± 1.9

15.2 ± 2.4

  

Down

29.4 ± 1.3

22.2 ± 1.1

18.2 ± 2.3

6.6 ± 1.5

16.4 ± 2.4