Table 2

Prior knowledge

Regulator

Target

Interaction

Source

Score

Reference


HapX

sreA

repression

1

0.5

[29]

HapX

AFUA_5G10610

interaction

2

0.25

[32]

HapX

mirB

activation

1,3

0.625

[32,51]

HapX

hemA

repression

2

0.25

[32]

HapX

sdh2

repression

2

0.25

[32]

input

sreA

activation

2

0.25

[31]

input

hapX

repression

2

0.25

[32]

PacC

mirB

interaction

3

0.125

[46]

PacC

ftrA

interaction

3

0.125

[46]

PacC

hem13

interaction

3

0.125

[46]

SreA

sdh2

repression

2

0.25

[31]

SreA

hemA

repression

2

0.25

[31]

SreA

AFUA_5G10610

repression

2

0.25

[31]

SreA

hapX

repression

1,3

0.625

[31]

SreA

mirB

repression

1

0.5

[31]

SreA

ftrA

repression

1,3

0.625

[31]

SreA

sidL

repression

3

0.125

[31]


SrbA

hapX

activation

1

0.5

[37]

SrbA

ftrA

activation

1

0.5

[37]

SrbA

mirB

activation

1

0.5

[37]

SrbA

hem13

activation

1

0.5

[37]

SreA

hem13

no interaction

1

0.5

[37]


The table lists regulator-target gene interactions, the type of interaction, the source of prior knowledge, the score used and references. The second part of the table lists additional prior knowledge we exploited in order to refine the model within the second round of modelling. "Input" denotes the fact that a target gene is regulated by the external perturbation (shift from iron replete to iron depleted conditions).

Linde et al. BMC Systems Biology 2012 6:6   doi:10.1186/1752-0509-6-6

Open Data