Table 3

Revised Boolean functions for the simulation of TGFβ1 stimulation.

1

COL1A1.out

= TGFB1 OR FOS OR JUN

*

2

COL1A2.out

= (TGFB1 AND JUND) OR JUN

*

3

ETS1.out

= FOS AND NOT (TGFB1 AND SMAD4 AND NOT SMAD7)

*

4

FOS.out

= (TGFB1 OR (TNF AND NFKB1)) AND NOT (JUN AND FOS)

5

JUN.out

= (TNF AND JUN) OR (TGFB1 AND SMAD4 AND NOT SMAD7)

6

JUNB.out

= (TGFB1 AND NFKB1 AND SMAD4 AND NOT SMAD7) OR (TNF AND NFKB1)

7

JUND.out

= TGFB1 OR TNF OR (JUND AND NOT FOS)

8

MMP1.out

= JUND AND NOT (TGFB1 AND FOS)

*

9

MMP3.out

= (TNF AND ((ETS1 AND NFKB1) OR JUN)) OR FOS

10

MMP9.out

= TNF AND ETS1 AND NFKB1

11

MMP13.out

= (TNF AND (JUN OR NFKB1)) OR FOS

12

NFKB1.out

= TNF OR ETS1 OR NFKB1

*

13

SMAD4.out

= TGFB1

*

14

SMAD7.out

= (TGFB1 AND SMAD4 AND NOT SMAD7) OR FOS OR JUN

*

15

TIMP1.out

= (TGFB1 AND SMAD4 AND NOT SMAD7) OR (TNF AND (JUN OR JUNB OR JUND OR NFKB1)) OR FOS

16

TGFB1.out

= FOS OR JUND

17

TNF.out

= TNF AND ((ETS1 AND NFKB1) OR JUN)

18

Inactivation rule

If the transcription factors ETS1, FOS, JUN or JUNB are expressed at t > 0, they will be down- regulated at t+3 and afterwards.

Rows marked by an asterisk indicate differences of the functions for TGFβ1 and TNFα stimulation, changes to Table 2 are italicised and printed in bold. Function numbers in bold indicate omitted (1, 2, 3, 8, 9, 11, 12, 14) or inserted (18) terms.

Wollbold et al. BMC Systems Biology 2009 3:77   doi:10.1186/1752-0509-3-77