Table 5

Expression data for MADE example

Fold change

MADE states



Gene

1 → 2

P

2 → 3

P

3 → 1

P

1

2

3


g4

2.1

0.68

3.0

0.08

0.7

0.15

1

1

1

g5a

0.5

0.45

8.0

0.44

0.8

0.22

1

0

1

g5b

1.1

0.07

0.1

0.49

2.2

0.03

1

1

0

g6

3.6

0.05

1.6

0.22

0.4

0.48

0

1

1

g7a

1.4

0.38

4.2

0.40

1.8

0.43

1

1

1

g7b

2.3

0.04

0.4

0.19

0.3

0.12

1

1

1

g8a

1.3

0.40

7.3

0.21

0.2

0.45

0

0

1

g8b

0.9

0.89

4.1

0.83

0.1

0.28

0

0

1


Fold change and P-values for the MADE example. Column "1 → 2" and indicates the fold change in expression between conditions 1 and 2; P is the P-value for this change. "MADE states" are the binary gene states returned by the algorithm. The states maximize the transitions in the expression data while retaining model functionality in each condition. Gene names correspond to the network in Figure 5a. Results are also depicted in Figure 5d.

Jensen et al. BMC Systems Biology 2011 5:147   doi:10.1186/1752-0509-5-147

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