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Table 3 Revised Boolean functions for the simulation of TGFβ1 stimulation.

From: Adapted Boolean network models for extracellular matrix formation

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 .

  1. 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.