Fragmenting the early EGFR pathway

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Niveau: Supérieur, Master
Fragmenting the early EGFR pathway Jerome Feret March 2012 All along this pratical work, by “fragments”, we mean homogeneous frag- ments (ie. the fragments which can be generated from a non oriented contact map). Heterogeneous fragments are not implemented yet. 1 The model We consider the following rule set: r01: EGF ( r1 ) , EGFR ( l1,r ) ?? EGF (r ) , EGFR(l ,r ) r02: EGF (r ) , EGFR(l ,r ) ?? EGF ( r1 ) , EGFR ( l1,r ) r03: EGF ( r2 ) , EGF ( r1 ) , EGFR ( l2,r ) , EGFR ( l1,r ) ?? EGF ( r3 ) , EGF ( r2 ) , EGFR ( l3,r1 ) , EGFR ( l2,r1 ) r04: EGF ( r3 ) , EGF ( r2 ) , EGFR ( l3,r1 ) , EGFR ( l2,r1 ) ?? EGF ( r2 ) , EGF ( r1 ) , EGFR ( l2,r ) , EGFR ( l1,r ) r05: EGF ( r3 ) , EGF ( r2 ) , EGFR ( l3,r1 ) , EGFR ( Y68u,l 2,r1 ) ?? EGF ( r3 ) , EGF ( r2

  • fragment

  • egfr

  • reset-all

  • contact map given

  • final time

  • annotated contact map

  • contact map

  • kappa rule

  • output-scheme egfr


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Fragmenting the early EGFR pathway
J´erˆomeFeret March 2012 All along this pratical work, by “fragments”, we mean homogeneous frag-ments (ie. the fragments which can be generated from a non oriented contact map). Heterogeneous fragments are not implemented yet.
1Themodel
We consider the following rule set:    1 1 r01:EGF r,EGFR l,r−→EGF(r) ,EGFR(l,r)    1 1 r02:EGF(r) ,EGFR(l,r)−→EGF r,EGFR l,r        2 12 13 2 r03:EGF r,EGF r,EGFR l,r,EGFR l,r−→EGF r,EGF r,    3 12 1 EGFR l,r,EGFR l,r        3 23 12 12 1 r04:EGF r,EGF r,EGFR l,r,EGFR l,r−→EGF r,EGF r,    2 1 EGFR l,r,EGFR l,r      3 23 12 13 r05:EGF r,EGF r,EGFR l,r,EGFR Y68,l,r−→EGF r, u     2 31 21 EGF r,EGFR l,r,EGFR Y68,l,r p   r06:EGFR Y68−→EGFR(Y68) p u      3 23 12 13 r07:EGF r,EGF r,EGFR l,r,EGFR Y48,l,r−→EGF r, u     2 31 21 EGF r,EGFR l,r,EGFR Y48,l,r p   r08:EGFR Y48−→EGFR(Y48) p u      11 11 r09:EGFR Y48,r,SHC Y7,pi−→EGFR Y48,r,SHC Y7,pi p up p   − − r10:SHC Y7,pi−→SHC(Y7,pi) p u   r11:SHC Y7,pi−→SHC(Y7,pi) p u     1 1 r12:EGFR Y68,GRB2(a,b)−→EGFR Y68,GRB2 a,b p p     1 1 r13:EGFR Y68,GRB2 a,b−→EGFR Y68,GRB2(a,b) p p     1 1r14:EGFR Y68,GRB2(a,b)−→EGFR Y68,GRB2 a,b p p     1 1− − r15:EGFR Y68,GRB2 a,b−→EGFR Y68,GRB2(a,b) p p      1 12 21 r16:EGFR Y68,GRB2 a,b,SOS(d)−→EGFR Y68,GRB2 a,b, p p   1 SOS d       2 21 11 1 r17:EGFR Y68,GRB2 a,b,SOS d−→EGFR Y68,GRB2 a,b, p p SOS(d)    1 1 r18:GRB2(a,b) ,SOS(d)−→GRB2 a,b,SOS d    1 1 r19:GRB2 a,b,SOS d−→GRB2(a,b) ,SOS(d)      1 12 12 r20:GRB2 a,b,SHC Y7,pi,SOS(d)−→GRB2 a,b,SHC Y7,pi, p p   1 SOS d