Adapted Boolean network models for extracellular matrix formation

BMC Systems Biology

Table 4 Revised Boolean functions for the simulation of TGFα stimulation.

1	COL1A1.out	= (FOS OR JUN) AND NOT (TNF AND ETS1 *AND* NFKB1)	*
2	COL1A2.out	= JUN AND NOT (TNF AND ETS1 *AND* NFKB1)	*
3	ETS1.out	= (TNF AND (ETS1 OR JUN)) OR FOS	*
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	= (TNF AND ETS1 *AND* NFKB1) OR FOS OR JUND	*
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 AND (ETS1 OR NFKB1)	*
13	SMAD4.out	= *TRUE*	*
14	SMAD7.out	= (FOS OR JUN) AND NOT (TNF AND NFKB1)	*
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, 8, 9, 11, 12, 13, 14) or inserted (18) terms.

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