=mtorr    
!rasgap+sos1=ras    Interaction with SOS1 increases the rate of GDP/GTP exchange of Ras (and thus acts as activating GEF) (Li et al, 1993). The GTPase activating protein RasGAP leads to hydrolysis of Ras-bound GTP to GDP (Cox and Der, 2003).;:; 
!p90rskerk12d+grb2+sos1r=sos1    Sos1 is bound to Grb2. Binding of Grb2 to EGFR, either directly or indirectly through Shp, leads to activation of Sos. Serine/threonine phosphorylation of Sos by P90rsk and Erk1/2 causes dissociation of Grb2-Sos from Shp or from the phosphorylated receptor (Douville & Downward, 1997). 
pip3+pi3kr+eps8r+sos1r=sos1_eps8_e3b1    SOS1, Eps8 and E3b1/Abi1 form a complex which is necessary for the Rac-GEF activity of SOS1. Furthermore, binding of the p85 subunit of PI3K to the complex is required for a basal Rac-GEF activity, which is increased by PIP3 (Innocenti et al, 2003). Note that this reaction differs from the description in the map of Oda et al: There, only Ras-activated PI3K influences the GEF-activaty, whereas we assume the inactivated form to mediate this effect. Additionally, the influence of PIP3 is not considered in the map of Oda et al. 
ship2=ship2d    
shc=grb2    Grb2 can bind to ErbB-dimers via Shc (Okabayashi et al, 1994). 
rin1+!rntre=rab5a    RIN1 mediates GDP/GTP exchange for Rab5a thus activating it (Tall et al, 2001). The GTPase activating protein RN-tre acts on Rab5a and inhibits internalization of EGFR (Lanzetti et al, 2000). 
mtorr+rheb=mtor_rap    
ras=rin1    Rab5-GEF activity of RIN1 is potentiated by activated Ras (Tall et al, 2001). 
pi3kr+ras=pi3k    GTP-bound Ras activates PI3K (Downward 1998). ;:; 
!aktd+pak1+ras=raf1    
!aktd+csrc+ras=raf1    Ras recruits Raf1 to the plasma membrane where it is phosphorylated at various sites. Src phosphorylates Raf1 on Y341, Pak1 phosphorylates S338, whereas it seems as if phosphorylation of either S338 or Y341 is sufficient for Raf1 activation. However, both kinases lead to different activation levels of Raf1 (the highest to be achieved in combination) that might stimulate different biological outcomes (King et al, 2001).;:; 
rac_cdc42=mlk3    MLK3 binds GTP-bound Cdc42/Rac and is thus activated (Vacratsis et al, 2002).;:; 
rac_cdc42=mekk4    MEKK4 contains a Cdc42/Rac interactive binding motif and is activated after binding to Cdc42/Rac. This binding is independent of the nucleotide bound to Cdc42/Rac, thus MEKK4 can be activated by the GDP-and GTP-bound protein (Schlesinger et al, 1998). Perhaps a different activation for Cdc42/Rac is necessary for binding MEKK4. We included only binding to the GTP-bound state in the model so far.  
rac_cdc42=mekk1    MEKK1 binds Cdc43/Rac and is thus activated (Schlesinger et al, 1998). Auto-ubiquitination of MEKK1 leads to degradation and therefore downregulates activation of downstream targets (Witowsky and Johnson, 2003). That is why we should think about setting this activation to zero after some time.  
pten=ptend    
plcg=ip3    
plcg=dag    PLCgamma hydrolyzes PI(4,5)P2 to generate DAG and IP3 (Kim et al, 2000). At present, we do not consider PLCbeta (as depicted in Oda et al), since this is part of the G-coupled receptor signaling. 
pip3=gab1    PIP3 recruits Gab1 molecules to the EGFR and thus enhances the activity of Gab1 (Rodrigues et al, 2000). As we do not consider multilevel activation, we decided to exclude this positive feedback loop in the logical analysis. For the analysis of the interaction graph, we assume that the reaction is time delayed as it is part of a (positive) feedback loop  
mtor_ric+!pp2a+pip3+pdk1=akt    PIP3 or PI(3,4)P2 recruit Akt and PDK1 to the plasma membrane. At the membrane, the HM region of Akt is phosphorylated at S473, probably by the Rictor-mTOR complex (Sarbassov et al, 2005). The phosphorylated HM region of PKB stabilizes PDK1 so that PDK1 can phosphorylate T308 of PKB (Scheid and Woodgett, 2003). PP2A dephosphorylates Akt (Andjelkovic et al, 1996). ;:; 
pi3k+ship2d+!ptend=pi34p2    
!ship2d+!ptend+pi3k=pip3    PI3K phosphorylates PI(4,5)P2 at the D3 position and thus generates PI(3,4,5)P2 (Vanhaesobroeck et al, 1997). Since PI(4,5)P2 is one of the major phosphorylated forms of PtdIns (Tolias and Cantly, 1999) we assume that it is always present in the cell and do not consider its regulation. PTEN dephosphorylates PI(3,4,5)P3 at the D3 position, SHIP catalyzes the dephosphorylation at D5 (Scheid and Woodgett, 2003). 
=pi3kr    
mtor_ric+pi34p2+!pp2a+pdk1=akt    
ca+dag+pdk1=pkc    PKC is phosphorylated at its activation loop by PDK1. This leads to autophosphorylation and the release of PKC into the cytoplasma. A pseudosubstrate is bound to the substrate-binding cavity, which is released after binding to the second messengers Ca2+ and DAG (Newton, 2003). Note that the influence of calcium ions on this reaction is not part of the map of Oda et al.  
pak1=limk1    PAK1 (activated through Rac/Cdc42) phosphorylates LIMK1 at T508 (Edwards et al, 1999).  
p90rsk=creb    p90RSK phosphorylates CREB on S133 and thus activates it (De Cesare et al, 1998).;:; 
erk12+p90rsk=p90rskerk12d    Reaction that is introduced for modeling the time delay p90RSK and ERK1/2 phosphorylate and thus inhibit SOS1 with. In the logical analysis, we use an incomplete truth table for this reaction, because we do not know whether both kinases are necessary for the inhibition or if one suffices.;:; 
mtor_rap+p70s6_1+pdk1=p70s6_2    
p38=mk2    MK2 binds to and is phosphorylated by p38 (Gaestel 2006).;:; 
stat5=    
stat3=    
stat1=    
pkc=    
p70s6_2=    
hsp27=    
elk1=    
creb=    
cmyc=    
pro_apoptotic=    
ap1=    
actin_reorg=    
nucerk12+!pp2b=elk1    ERK1/2 phosphorylates Elk1 at S383 and S389 (Cavigelli et al, 1995). PP2B dephosphorylates ELK1 (Tian and Karin, 1999). In (Tian and Karin, 1999) activation of Elk1 through other MAPKs is also mentioned. However, for phosphorylating transcription factors translocation to the nucleus is necessary, which is stimulated in the case of JNK by UV-irradiation (Cavigelli et al, 1995). ;:; 
!gsk3+nucerk12=cmyc    ERK1/2 phosphorylates c-Myc at S62 and thus stabilizes it. The phosphorylation of S62 is necessary for the phosphorylation of T58 by GSK3 beta, which leads to ubiquitin dependent degradation of c-Myc (Sears, 2000). GSK3 beta is not included in Oda et al. ;:; 
!tsc1_tsc2=rheb    
!akt+!pak1=bad    PAK1 phosphorylates Bad on S112 and S136, independently of PI3K (Schuermann et al, 2000). Akt phosphorylates Bad on S136. In some cell types (e. g. cerebellar granule cells) this suffices for inhibiting apoptosis. However, in other cell types (e. g. Il-3 dependent hematopoietic cells) Bad must be phosphorylated on S136 and S112 (Datta et al, 2000). ;:; 
!akt+!p90rsk=gsk3    p90Rsk phosphorylates Gsk3 on S0 and thus deactivates it in response to EGF. Akt also phosphorylates S9, however, we are not sure whether this occurs only in response to insulin. Other kinases, like p70s6 and PKC, are also known to deactivate Gsk3; however, not in all cell types and not in response to EGF, so their influence has to be further studied before including it in the model (Grimes and Jope, 2001).  
nck+rac_cdc42=pak1    
mlk3=mkk6    
mlk3=mkk3    MLK3 phosphorylates and thus activates MKK3 and MKK6 (Tibbles et al, 1996). ;:; 
mkk4+mkk7=jnk    MKK4 and MKK7 cooperate to activate JNK. MKK4 phosphorylates Y185, MKK7 phosphorylates T183 (Kishimoto et al, 2003). 
mk2=hsp27    MK2 phosphorylates Hsp27 on S15, S78 and S82 (Stokoe et al, 1992).;:; 
mk2=creb    MK2 phosphorylates and thus activates CREB at S133 (Tan et al, 1996) 
mekk1=mkk7    MEKK1 phosphorylates and thus activates MKK7 (Lu et al, 1997). ;:; 
mek12=erk12    MEK1 and MEK2 phosphorylate ERK1/2 (Robinson & Cobb, 1997).;:; 
limk1=actin_reorg    LIMK1 phosphorylates cofilin, thereby leading to accumulation of actin filaments and aggregates (Edwards et al, 1999). ;:; 
jnk=p70s6_1    
jnk=cjun    JNK phosphorylates c-jun. Unphosphorylated c-jun is ubiquitinated and degraded. Phosphorylation by JNK also increases the transriptional activity of c-jun (Karin et al, 1997). Regulation of transcription of c-jun is not considered here, this could be included in a model regarding multi-level activation.  
jnk+!pp2a=cfos    jnk phosphorylates cfos and thus prevents it from degradation (Coronella-Wood et al, 2004). Note that this reaction is independent of erk (Coronella-Wood et al, 2004). PP2A dephosphorylates cfos, whereas PP2B does not (Coronella-Wood, 2004) inconsistent with Oda's map. Regulation of transcription of cfos is not considered here, this could be included in a model regarding multi-level activation.   
ip3=ca    Binding of IP3 to its receptor at the endoplasmatic reticulum leads to Ca2+ release into the cytosol (Alberts et al, 2004), (Kim et al, 2000). 
=tgfa    
=sos1r    
=ship2    
=pten    PTEN and SHIP2 both down regulate PIP3 synthesis. As we could not find any information how PTEN and SHIP2 are regulated, we included them as inputs to the model. We suppose that down regulation of PI3K signaling is time delayed and therefore set the activation of PTEN and SHIP2 to time scale 2. 
=pp2b    Although PP2B is activated by Ca2+ (which is part of the model), we decided not to consider its regulation, because activation of PP2B also depends on calmodulin (Ishida et al, 2003). ;:; 
=pp2a    
=pdk1    PDK1 appears to be constitutively active (Newton 2003) and is thus an input to the model. 
=nrg4    
=nrg3    
=nrg2b    
=nrg2a    
=nrg1b    
=nrg1a    
=mkp    
=hbegf    
=erbb4    
=erbb3    
=erbb2    
=erbb1    
=eps8r    
=epr    
=egf    
=csrc    
=btc    
=bir    
=ar    
grb2=gab1    Gab1 can bind to ErbB dimers via Grb2 (Rodrigues et al, 2000). 
rac_cdc42+grb2=pak1    Pak1 is recruited to the plasma membrane via Grb2 (Puto et al, 2003) or Nck (Li et al, 2001) where it is activated through GTP-bound Rac/Cdc42 (Edwards et al, 1999). Note that reaction 204 is not included in Oda et al.;:; 
gab1=shp2    Phosphorylated Gab1 recruits and activates SHP2. \cite{Montagner2005}.  
pi3kr+gab1=pi3k    Phosphorylated Gab1 recruits and activates PI3K (Montagner et al, 2005). Gab1 bound SHP2 dephosphorylates the PI3K binding site of Gab1. However, we decided not to include the negative influence of SHP2 on PI3K in the model so far, because it seems as if SHP2 indeed downregulates PI3K, but does not completely inhibit PI3K activation through Gab1 (Montagner et al, 2005, Zhang et al, 2002).) 
gab1+!shp2=rasgap    RasGAP can bind tyrosine phosphorylation sites on Gab1, Gab1-bound SHP2 dephosphorylates these sites (Montagner et al, 2005) . Note that this reaction is not part of the map of Oda et al.;:; 
erk12=p70s6_1    Phosphorylation of several S/T residues (S404, S411, S418, S424, T421) in the C-terminal autoinhibitory domain of p70s6 leads to a conformational change that enables the phosphorylation of the catalytic sites T389 and S229 (Berven and Crouch, 2000). Both JNK and ERK1/2 are able to phosphorylate the autoinhibitory sites (Mukhopadhyay et al, 1992). However, the mechanism of activation of these sites is not well understood and additional kinases are probably involved in this step (Berven and Crouch, 2000). We refer to p70s6 phosphorylated at the autoinhibitory sites as p70s6_1. mTOR phosphorylates p70s6 on T389 (Hou et al, 2007) and T229 is phosphorylated by PDK1 (Downward 1998), (Berven and Crouch, 2000).;:; 
pdk1+erk12=p90rsk    ERK1/2 and PDK1 activate P90RSK by phosphorylation. ERK1/2 activates the C-terminal domain, PDK1 the N-terminal domain (Ser227), whereas the first ist necessary for the latter (Froedin et al, 2005). 
erk12+p90rsk+!pp2a=cfos    erk and p90rsk coordinately phosphorylate cfos - unphosphorylated cfos is rapidly degraded (Murphy et al, 2002). Note that the influence of P90rsk is not depicted in Oda's map. PP2A dephosphorylates cfos, whereas PP2B does not (Coronella-Wood et al, 2004) inconsistent with Oda's map. Regulation of transcription of cfos is not considered here, this could be included in a model regarding multi-level activation.  
erk12+!mkp=nucerk12    MKP dephosphorylates ERK1/2 and thus inhibits phosphorylation of transription factors like Elk1 in the nucleus (Sun et al, 1993).;:; 
erbb44=nck    
erbb44=grb2    
erbb44=shc    
erbb34=shc    
erbb34+pi3kr=pi3k    
erbb34=grb2    
erbb24=shc    
erbb24=grb2    
csrc+erbb24=stat5    
erbb23=shc    
erbb23=grb2    
pi3kr+erbb23=pi3k    
erbb11=plcg    phospholipase c gamma is phosphorylated by ErbB1 at Y1254, Y783, Y771 and Y472 (Kim et al, 1990). 
erbb11=gab1    Gab1 can bind directly to ErbB1-receptors and is phosphorylated on Y-residues by the receptor kinase (Rodrigues et al, 2000).  
erbb11=shp1    SHP1 binds to ErbB1 at phosphorylated Y1173 (Keilhack et al, 1998). As phosphorylated SHP1 dephosphorylates the ErbB1 dimers (negative feedback), we assume that the activation occurs at time 2.  
erbb11=nck    
erbb11=grb2    Grb2 can bind to ErbB-dimers directly via its SH2 domain. As there are binding sites for Grb2 on all ErbB receptors (Schulze et al, 2005), we assume that Grb2 can directly interact with all possible ErbB-dimers.  
erbb14=shc    
erbb14=nck    
erbb14=grb2    
erbb13=shc    
erbb13=grb2    
pi3kr+erbb13=pi3k    In Oda et al (second figure) activation of PI3K through all ErbB3 and ErbB4 dimers is considered. Indeed there are binding sites for the p85 subunit of PI3K on both ErbB3 and ErbB4. However, there are 6 sites on ErbB3 and only one site on ErbB4, suggesting that ErbB3 is the main activator of PI3K (Olayioye et al, 2000). Furthermore, there are naturally occurring ErbB4 isoforms that do not contain the binding site for PI3K (Elenius et al, 1999). Thus we decided to include PI3K interaction only with ErbB3 dimers. 
erbb12=shc    
erbb12=grb2    
erbb11=shc    Shc binds to all types of ErbB-receptors. On ErbB1, the binding sites are pY1148 (via PTB domain) and pY1173 (via PTB and SH2 domain) (Olayioye et al, 2000).;:; 
csrc+erbb11=stat5    
csrc+erbb11=stat3    
csrc+erbb11=stat1    STAT1, 3 and 5 can be activated through ErbB1-homodimers whereas ErbB1 heterodimers do not seem to contribute to STAT activation. Neuregulin, which cannot activate ErbB1 dimers, induces activation of STAT5 through ErbB24. After ligand binding, Src is recruited to the activated receptor and phosphorylates receptor bound STATs on the consensus C-terminal Y-residue (Olayioye et al, 1999). It is not clear how Src is activated. Whereas in (Sato et al, 2005) activation of Src by Shc (in response to EGF) is reported that leads to phosphorylation of STAT, in (Olayioye et al, 1999) the activation of STAT after EGF stimulation was more rapid than activation of Src in response to EGF. Therefore we decided not to consider the influence of Shc on these reactions so far. 
erbb11+eps8r=rntre    RN-tre binds to the adaptor protein Eps8 and is phosphorylated in response to EGF stimulation (Lanzetti et al, 2000).;:; 
!endocyt_degrad=erbb11    
erbb11=ccbl    c-Cbl binds ErbB1 at pY1045, leading to degradation of the receptor in the lysosome (Citri and Yarden, 2006).;:; 
cjun+cfos=ap1    c-Jun and c-Fos heterodimerize and form the transcription factor AP-1 (Karin et al, 1997). ;:; 
rab5a+ccbl=endocyt_degrad    c-Cbl and Rab5a are both involved in the endocytic trafficking of ErbB receptors. c-Cbl is necessary for degradation of the receptors, while Rab5a controls the formation and fusion of endocytic vesicles (Citri and Yarden, 2006). As we are not sure whether both proteins are involved in the same pathway or in different trafficking routes, we use an incomplete truth table in the logical analysis of this reaction. 
bad=pro_apoptotic    Phosphorylation of Bad avoids its proapoptotic function (Schuermann et al, 2000). ;:; 
akt=aktd    Reaction that is only included for modeling the time delay Akt deactivates Raf1 with.;:; 
!akt=tsc1_tsc2    Akt phosphorylates Tsc2 and thus inhibits the Rheb-GAP activity of the Tsc1/Tsc2 complex. GTP-bound Rheb activates the mTOR-raptor complex (Hay and Sonenberg, 2004).;:; 
mtorr=mtor_ric    As the regulation of the mTOR-rictor complex is unknown (Sarbassov et al, 2005), we assume that it is only activated by its reservoir and therefore always active (comparable to an external input to the model). 
sos1_eps8_e3b1=rac_cdc42    
vav2=rac_cdc42    
raf1=mek12    
mekk1=mek12    
mkk4=p38    
mkk6=p38    
mkk3=p38    
mekk1=mkk4    
mlk3=mkk4    
mekk4=mkk4    
erbb11+pip3=vav2    
pi34p2+erbb11=vav2    
ar+erbb1+!shp1=erbb11    
bir+erbb1+!shp1=erbb11    
btc+erbb1+!shp1=erbb11    
bir+!shp1+erbb1+erbb2=erbb12    
btc+!shp1+erbb1+erbb2=erbb12    
egf+!shp1+erbb1+erbb2=erbb12    
epr+!shp1+erbb1+erbb2=erbb12    
hbegf+!shp1+erbb1+erbb2=erbb12    
!shp1+tgfa+erbb1+erbb2=erbb12    
erbb3+btc+!shp1+erbb1+!erbb2=erbb13    
erbb3+epr+!shp1+erbb1+!erbb2=erbb13    
erbb3+egf+!shp1+erbb1+!erbb2=erbb13    
erbb3+nrg1a+!shp1+erbb1+!erbb2=erbb13    
erbb3+nrg1b+!shp1+erbb1+!erbb2=erbb13    
erbb3+nrg2a+!shp1+erbb1+!erbb2=erbb13    
erbb3+tgfa+!shp1+erbb1+!erbb2=erbb13    
erbb3+ar+!shp1+erbb1=erbb13    
erbb4+epr+!shp1+erbb1+!erbb2=erbb14    
erbb4+egf+!shp1+erbb1+!erbb2=erbb14    
erbb4+nrg1a+!shp1+erbb1+!erbb2=erbb14    
erbb4+nrg1b+!shp1+erbb1+!erbb2=erbb14    
erbb4+nrg2a+!shp1+erbb1+!erbb2=erbb14    
erbb4+nrg4+!shp1+erbb1+!erbb2=erbb14    
erbb4+tgfa+!shp1+erbb1+!erbb2=erbb14    
erbb4+nrg2b+!shp1+erbb1+!erbb2=erbb14    
egf+erbb1+!shp1=erbb11    
epr+erbb1+!shp1=erbb11    
hbegf+erbb1+!shp1=erbb11    
tgfa+erbb1+!shp1=erbb11    
erbb3+bir+erbb2=erbb23    
erbb3+btc+erbb2=erbb23    
erbb3+epr+erbb2=erbb23    
erbb3+nrg1a+erbb2=erbb23    
erbb3+nrg1b+erbb2=erbb23    
erbb3+nrg2b+erbb2=erbb23    
erbb4+bir+erbb2=erbb24    
erbb4+btc+erbb2=erbb24    
erbb4+egf+erbb2=erbb24    
erbb4+epr+erbb2=erbb24    
erbb4+hbegf+erbb2=erbb24    
erbb4+nrg1a+erbb2=erbb24    
erbb4+nrg1b+erbb2=erbb24    
erbb4+nrg2a+erbb2=erbb24    
erbb4+nrg2b+erbb2=erbb24    
erbb4+nrg3+erbb2=erbb24    
erbb4+nrg4+erbb2=erbb24    
erbb4+erbb3+nrg2a+!erbb2=erbb34    
erbb4+erbb3+nrg1a+!erbb2=erbb34    
erbb4+erbb3+nrg1b+!erbb2=erbb34    
erbb4+erbb3+nrg2b+!erbb2=erbb34    
erbb4+bir=erbb44    
erbb4+btc=erbb44    
erbb4+nrg1a=erbb44    
erbb4+nrg1b=erbb44    
erbb4+nrg2b=erbb44    
erbb4+nrg3=erbb44    
erbb4+nrg4=erbb44    
erbb4+erbb2+tgfa=erbb24    
