Fragmenting the early EGFR pathway

Jérôme Feret

Description

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

Sujets

• Fragment

Informations

• Publié par: profil-mupheg-2012
• Nombre de lectures: 14
• Langue: English

Extrait

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      1−1 1−1 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 1− r14: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