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Table 2 Update rules of model species and supporting literature citations

From: Iron acquisition and oxidative stress response in aspergillus fumigatus

Update rules Literature support
1 hapX(t+1) = NOT SreA Transcription of hapX is repressed by SreA [13,29].
2 sreA(t+1) = NOT HapX Transcription of sreA is repressed by HapX [13,29].
3 HapX(t+1) =hapX AND (NOT LIP) An ortholog of HapX is inactivated by intracellular iron [58].
4 SreA(t+1) =sreA AND LIP An ortholog of SreA is activated by intracellular iron [59,60].
5 RIA(t+1) = NOT SreA SreA transcriptionally represses RIA genes [13].
6 EstB(t+1) = NOT SreA SreA transcriptionally represses estB [13].
7 MirB(t+1) = HapX AND (NOT SreA) HapX transcriptionally activates mirB [29]. SreA transcriptionally represses mirB [13].
8 SidA(t+1) = HapX AND (NOT SreA) HapX up regulates the SidA substrate ornithine [29]. SreA transcriptionally represses sidA [13].
9 TAFC(t+1) = SidA SidA catalyzes the first step in siderophore biosynthesis [5,8]
10 ICP(t+1) = (NOT HapX) AND (VAC OR FC +Fe) HapX represses consumption of intracellular iron [29].
11 LIP(t+1) = (TAFC AND MirB AND EstB) OR (Iron AND RIA) TAFC sequesters iron from the extracellular space [8]. MirB imports ferri-TAFC [54]. EstB
  degrades ferri-TAFC bonds and releases free iron [55]. RIA compensates for a lack of
  siderophores when grown in high iron media [33].
12 CccA(t+1) = NOT HapX HapX transcriptionally represses cccA [29].
13 FC Fe(t+1) = SidA SidA catalyzes the first step in siderophore biosynthesis [5,8]
14 FC +Fe(t+1) = LIP AND FC Fe FC is involved in intracellular iron storage [14,49].
15 VAC(t+1) = LIP AND CccA CccA mediates import of intracellular iron into the vacuole [56].
16 ROS(t+1) = LIP OR Elevated free iron levels catalyze the formation of ROS [63].
\(\left ({\vphantom {\sum \limits ^{1}_{1}}}\; \text {Superoxide AND}\; \left ({\vphantom {\frac {\sum }{\sum }}}\; \text {NOT (SOD3 AND ThP AND Cat1/2)}\; \right)\; \right)\) OR SODs convert O\(_{2}^{-}\) to H 2 O 2 [20]. Either catalases or thioredoxin
\(\left ({\vphantom {\sum \limits ^{1}_{1}}}\; \text {ROS AND} \left ({\vphantom {\frac {\sum }{\sum }}}\; \text {NOT} \left ({\vphantom {\frac {1}{2}}}\; \text {SOD3 AND (ThP OR Cat1/2)}\; \right)\; \right)\; \right)\) convert H 2 O 2 to non-reactive H 2O [9,64].
17 Yap1(t+1) = ROS Yap-1 is activated by superoxide [61,62].
18 SOD2/3(t+1) = Yap1 Yap-1 activates transcription of sod2/3 [61].
19 Cat1/2(t+1) = Yap1 AND (NOT HapX) Yap-1 activates transcription of cat1/2 [61]. HapX transcriptionally represses cat1 [29].
20 ThP(t+1) = Yap1 Yap-1 activates transcription of thioredoxin peroxidases [61].
21 Iron(t+1) = Iron External parameter.
22 Superoxide(t+1) = Superoxide [ = NOT Superoxide, Figure 5 only] External parameter.
  1. Species that appear on the right side of the = represent states at time t.